3CLT

Crystal structure of the R236E mutant of 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
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.692α = 90
b = 116.692β = 90
c = 84.412γ = 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
122099.90.06211.24.54178241782

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 SYNTHESISTHROUGHOUT1O97219.9141782220999.950.154920.153260.18607RANDOM22.176
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]
0.160.080.16-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.669
r_dihedral_angle_4_deg18.238
r_dihedral_angle_3_deg13.149
r_dihedral_angle_1_deg6.15
r_scangle_it2.199
r_scbond_it1.409
r_angle_refined_deg1.301
r_mcangle_it0.889
r_angle_other_deg0.797
r_mcbond_it0.608
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.669
r_dihedral_angle_4_deg18.238
r_dihedral_angle_3_deg13.149
r_dihedral_angle_1_deg6.15
r_scangle_it2.199
r_scbond_it1.409
r_angle_refined_deg1.301
r_mcangle_it0.889
r_angle_other_deg0.797
r_mcbond_it0.608
r_symmetry_vdw_other0.219
r_nbd_refined0.199
r_nbd_other0.18
r_nbtor_refined0.167
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.133
r_mcbond_other0.109
r_nbtor_other0.081
r_chiral_restr0.076
r_symmetry_vdw_refined0.068
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms4243
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling