4A6G

N-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SJAPDB ENTRY 1SJA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18PROTEIN CONCENTRATION OF 8 MG ML-1 THAT HAD BEEN INCUBATED PREVIOUSLY WITH 10 MM N-ACETYL METHIONINE. CRYSTAL DROPS CONTAINED 100 MM TRIS-HCL (PH 8.0) 15% PEG 4K, 800 MM NA FORMATE
Crystal Properties
Matthews coefficientSolvent content
3.7467.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 216.71α = 90
b = 216.71β = 90
c = 261.1γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2011-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
12.7188.311000.0818.610.2606934.8
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)
12.712.791000.54.810.4

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 1SJA2.7188.3160693322699.970.158160.155350.21012RANDOM47.754
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]
-0.2-0.1-0.20.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.304
r_dihedral_angle_4_deg23.185
r_dihedral_angle_3_deg20.631
r_dihedral_angle_1_deg6.891
r_angle_refined_deg2.097
r_chiral_restr0.138
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.304
r_dihedral_angle_4_deg23.185
r_dihedral_angle_3_deg20.631
r_dihedral_angle_1_deg6.891
r_angle_refined_deg2.097
r_chiral_restr0.138
r_bond_refined_d0.02
r_gen_planes_refined0.01
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms10897
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing