5MHB | pdb_00005mhb

Product-Complex of E.coli 5-Amino Laevulinic Acid Dehydratase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B4E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2293ALAD at 7 mg per ml mixed with equal volume of well solution: 200 mM Tris pH 8.0 - 8.4, 2 % saturated Ammonium sulphate, 200 microM zinc sulphate, 6 mM beta-mercaptoethanol and 3 mM porphobilinogen. Crystals were grown in the dark.
Crystal Properties
Matthews coefficientSolvent content
4.1470.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.619α = 90
b = 128.619β = 90
c = 142.815γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate1997-11-06MSINGLE WAVELENGTH
21x-ray100IMAGE PLATEMAR scanner 300 mm plate1998-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.069ESRFBM14
2SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.834EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
22.0723.8495.20.0780.99815.3734487
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.072.1968.10.3680.9113.24.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1b4e2.195.5732987176198.950.159530.156760.170.212850.22RANDOM34.462
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.620.62-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.421
r_dihedral_angle_4_deg19.411
r_dihedral_angle_3_deg14.638
r_long_range_B_refined7.634
r_long_range_B_other7.391
r_dihedral_angle_1_deg6.664
r_scangle_other4.7
r_scbond_it3.005
r_scbond_other2.922
r_mcangle_it2.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.421
r_dihedral_angle_4_deg19.411
r_dihedral_angle_3_deg14.638
r_long_range_B_refined7.634
r_long_range_B_other7.391
r_dihedral_angle_1_deg6.664
r_scangle_other4.7
r_scbond_it3.005
r_scbond_other2.922
r_mcangle_it2.894
r_mcangle_other2.893
r_angle_refined_deg2.541
r_mcbond_it1.933
r_mcbond_other1.933
r_angle_other_deg1.346
r_chiral_restr0.162
r_bond_refined_d0.028
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2484
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms37

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement