1W62

proline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W61PDB ENTRY 1W61

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.615% PEG 4000,100MM NH4ACETATE 50MM NA3CITRATE.H2O,PH5.6, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
2.653.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.018α = 90
b = 89.382β = 125.98
c = 84.456γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYERMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.56097.60.08102.427664254.3
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)
12.52.6497.40.2242.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1W612.53024875277897.30.1770.170.236RANDOM37.8
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]
-0.13-0.66-0.38-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_dihedral_angle_3_deg17.165
r_dihedral_angle_4_deg15.459
r_dihedral_angle_1_deg7.114
r_scangle_it2.967
r_scbond_it1.875
r_angle_refined_deg1.766
r_mcangle_it1.201
r_mcbond_it1.011
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.371
r_dihedral_angle_3_deg17.165
r_dihedral_angle_4_deg15.459
r_dihedral_angle_1_deg7.114
r_scangle_it2.967
r_scbond_it1.875
r_angle_refined_deg1.766
r_mcangle_it1.201
r_mcbond_it1.011
r_angle_other_deg0.88
r_symmetry_hbond_refined0.287
r_symmetry_vdw_refined0.219
r_symmetry_vdw_other0.217
r_nbd_refined0.208
r_nbd_other0.185
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.179
r_chiral_restr0.099
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5395
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing