3ILF

Crystal structure of porphyranase A (PorA) in complex with neo-porphyrotetraose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6295PEG 4000, Ammoniumsulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4449.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.09α = 90
b = 68.378β = 90
c = 71.268γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.849.3494.60.0620.05720.86.727062270621111.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.991.40.2120.1958.46.23741

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.849.3412706225651138193.950.159650.159650.157180.20461RANDOM13.339
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]
0.22-0.19-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.814
r_dihedral_angle_3_deg13.79
r_dihedral_angle_4_deg11.31
r_dihedral_angle_1_deg7.772
r_scangle_it4.909
r_scbond_it3.162
r_angle_refined_deg2.302
r_mcangle_it2.076
r_mcbond_it1.266
r_chiral_restr0.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.814
r_dihedral_angle_3_deg13.79
r_dihedral_angle_4_deg11.31
r_dihedral_angle_1_deg7.772
r_scangle_it4.909
r_scbond_it3.162
r_angle_refined_deg2.302
r_mcangle_it2.076
r_mcbond_it1.266
r_chiral_restr0.374
r_bond_refined_d0.026
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2109
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms73

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling