6SVF

Crystal structure of the P235GK mutant of ArgBP from T. maritima


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GGP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293protein concentration in the range 6-10 mg/ml in a solution containing 2.0 M ammonium sulfate and 5 % (v/v) 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.72α = 90
b = 52.964β = 90
c = 95.686γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442017-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.63097.50.070.080.03710.93.430630
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6570.2580.3450.227

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 REPLACEMENTTHROUGHOUT6GGP1.63029166142097.40.1730.17090.2175RANDOM14.06
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
r_dihedral_angle_2_deg28.549
r_dihedral_angle_4_deg15.625
r_dihedral_angle_3_deg12.237
r_dihedral_angle_1_deg5.837
r_angle_refined_deg2.032
r_angle_other_deg1.05
r_chiral_restr0.132
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.549
r_dihedral_angle_4_deg15.625
r_dihedral_angle_3_deg12.237
r_dihedral_angle_1_deg5.837
r_angle_refined_deg2.032
r_angle_other_deg1.05
r_chiral_restr0.132
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1798
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
EVAL15data reduction
EVAL15data scaling
MOLREPphasing