8PUQ

MetHemoglobin structure from serial synchrotron crystallography with fixed target


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.5293.1526%v PEG3350, 10mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8256.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.53α = 90
b = 63.08β = 111.02
c = 54.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293.15PIXELDECTRIS EIGER X 16M2021-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9762MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (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
11.9553.551000.99030.07510.617625258
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.020.75930.41941.37

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.9553.552525812111000.1270.12520.174163.641
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]
0.3981.89-2.0540.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.422
r_dihedral_angle_3_deg15.414
r_dihedral_angle_2_deg12.253
r_lrange_other10.449
r_lrange_it10.448
r_scangle_other9.661
r_scangle_it9.654
r_scbond_it6.95
r_scbond_other6.93
r_dihedral_angle_1_deg5.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.422
r_dihedral_angle_3_deg15.414
r_dihedral_angle_2_deg12.253
r_lrange_other10.449
r_lrange_it10.448
r_scangle_other9.661
r_scangle_it9.654
r_scbond_it6.95
r_scbond_other6.93
r_dihedral_angle_1_deg5.878
r_mcangle_it5.156
r_mcangle_other5.154
r_mcbond_it4.373
r_mcbond_other4.356
r_angle_refined_deg2.037
r_angle_other_deg0.843
r_nbd_refined0.208
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.153
r_symmetry_nbd_other0.142
r_symmetry_xyhbond_nbd_refined0.114
r_symmetry_nbd_refined0.112
r_chiral_restr0.106
r_nbd_other0.104
r_symmetry_nbtor_other0.068
r_bond_refined_d0.015
r_gen_planes_refined0.013
r_gen_planes_other0.007
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2180
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing