1OBI

Crystal structure of the G130A mutant of Malonamidase E2 from Bradyrhizobium japonicum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GR8PDB ENTRY 1GR8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720% POLYETHYLENE GLYCOL 1000, 0.1 M TRIS-HCL, PH 7.0
Crystal Properties
Matthews coefficientSolvent content
239.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.728α = 90
b = 94.762β = 90
c = 74.698γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.23090.70.066154382091
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2879.30.25432.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIRECT METHODSTHROUGHOUTPDB ENTRY 1GR82.23013452590.70.1720.1720.24RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_deg1.262
c_bond_d0.0049
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_deg1.262
c_bond_d0.0049
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6128
Nucleic Acid Atoms
Solvent Atoms847
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing