1HKW | pdb_00001hkw

MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LysA)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.54 UL HANGING DROPS (2 UL OF DAPDC 10 MG/ML CONTAINING 5MM OF LYSINE COMBINED WITH 2 UL OF WELL SOLUTION) WERE EQUILIBRATED AGAINST 500 UL OF WELL SOLUTION (24% PEG-MME 5K, 0.1M MES BUFFER PH6.3 AND 60 MM AMMONIUM SULFATE), pH 6.50
Crystal Properties
Matthews coefficientSolvent content
4.170

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.56α = 90
b = 111.56β = 90
c = 237.673γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCDMIRROR2002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-BAPS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.865.799.90.02828.222.6813664
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.8799.80.1367.522

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.8253585518861000.1950.1930.20310.248RANDOM38.37
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]
0.260.26-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.849
r_scangle_it4.744
r_scbond_it2.847
r_mcangle_it1.788
r_angle_refined_deg1.699
r_mcbond_it0.98
r_angle_other_deg0.974
r_nbd_other0.267
r_symmetry_vdw_other0.264
r_nbd_refined0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.849
r_scangle_it4.744
r_scbond_it2.847
r_mcangle_it1.788
r_angle_refined_deg1.699
r_mcbond_it0.98
r_angle_other_deg0.974
r_nbd_other0.267
r_symmetry_vdw_other0.264
r_nbd_refined0.237
r_symmetry_hbond_refined0.228
r_xyhbond_nbd_refined0.173
r_chiral_restr0.162
r_symmetry_vdw_refined0.112
r_nbtor_other0.106
r_bond_refined_d0.03
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6641
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms10

Software

Software
Software NamePurpose
TEXTALmodel building
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
DMphasing
TEXTALphasing
REFMACrefinement