4CMD

The (R)-selective transaminase from Nectria haematococca


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WRVPDB ENTRY 1WRV

Crystallization

Crystal Properties
Matthews coefficientSolvent content
359.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.062α = 90
b = 133.894β = 90
c = 61.666γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.6829.998.80.113.95.6935642
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)
11.681.7394.30.842.25.2

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 1WRV1.6883.1493564494198.60.159650.158140.18796RANDOM20.754
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]
-0.482.21-1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.157
r_dihedral_angle_4_deg17.235
r_dihedral_angle_3_deg13.142
r_dihedral_angle_1_deg5.347
r_scbond_it3.696
r_mcangle_it3.67
r_mcbond_it2.763
r_angle_refined_deg1.386
r_chiral_restr0.096
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.157
r_dihedral_angle_4_deg17.235
r_dihedral_angle_3_deg13.142
r_dihedral_angle_1_deg5.347
r_scbond_it3.696
r_mcangle_it3.67
r_mcbond_it2.763
r_angle_refined_deg1.386
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.007
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_mcangle_other
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 Atoms5096
Nucleic Acid Atoms
Solvent Atoms1085
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing