3CLU

Crystal structure of the R236K mutant from Methylophilus methylotrophus ETF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O97 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.2limited digest with trypsin, 2.0 M sodium phosphate, pH 6.2, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.6353.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.482α = 90
b = 116.482β = 90
c = 84.281γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.819990.0679.24.25820358203

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1O971.81952470279392.450.169630.16780.20395RANDOM31.954
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]
1.420.711.42-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.046
r_dihedral_angle_4_deg20.607
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg6.373
r_scangle_it3.037
r_scbond_it1.968
r_angle_refined_deg1.541
r_mcangle_it1.19
r_angle_other_deg0.825
r_mcbond_it0.815
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.046
r_dihedral_angle_4_deg20.607
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg6.373
r_scangle_it3.037
r_scbond_it1.968
r_angle_refined_deg1.541
r_mcangle_it1.19
r_angle_other_deg0.825
r_mcbond_it0.815
r_symmetry_hbond_refined0.255
r_symmetry_vdw_other0.25
r_nbd_refined0.209
r_mcbond_other0.2
r_nbd_other0.19
r_nbtor_refined0.177
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.141
r_chiral_restr0.089
r_nbtor_other0.088
r_bond_refined_d0.013
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4213
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling