5MJD

metNgb under oxygen at 80 bar


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OJ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6M AMMONIUM SULPHATE, 0.1M MES,PH6.5, 10%(V/V) DIOXANE
Crystal Properties
Matthews coefficientSolvent content
2.448.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.819α = 90
b = 87.819β = 90
c = 113.522γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rBENT MIRROR2016-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.8859ESRFBM30A

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
11.745.4995.60.053165.81023281769724
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)
11.71.893.70.4753.25.62592

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 SYNTHESISTHROUGHOUT1OJ61.7201685383094.740.181530.178880.24172RANDOM32.873
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]
0.110.050.11-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.117
r_dihedral_angle_4_deg16.968
r_dihedral_angle_3_deg14.216
r_long_range_B_refined7.352
r_long_range_B_other7.213
r_dihedral_angle_1_deg5.392
r_scangle_other5.291
r_mcangle_it4.114
r_mcangle_other4.111
r_scbond_other3.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.117
r_dihedral_angle_4_deg16.968
r_dihedral_angle_3_deg14.216
r_long_range_B_refined7.352
r_long_range_B_other7.213
r_dihedral_angle_1_deg5.392
r_scangle_other5.291
r_mcangle_it4.114
r_mcangle_other4.111
r_scbond_other3.278
r_scbond_it3.274
r_mcbond_it2.702
r_mcbond_other2.693
r_angle_other_deg2.013
r_angle_refined_deg1.779
r_chiral_restr0.116
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing