8PUR

DexyHemoglobin structure from serial synchrotron crystallography with fixed target


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.5293.1526%v PEG3350, 10mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.856.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.29α = 90
b = 63.06β = 111.01
c = 54.75γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293.15PIXELDECTRIS EIGER X 16M2021-03-07MSINGLE 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)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
11.8553.5041000.991412.4820529515
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9160.90492.9

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-VALUE1.8553.5042951514741000.1320.12990.162270.77
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]
0.4931.674-1.483-0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.925
r_dihedral_angle_3_deg14.561
r_dihedral_angle_2_deg12.972
r_lrange_other12.391
r_lrange_it12.388
r_scangle_other11.722
r_scangle_it11.719
r_scbond_it8.357
r_scbond_other8.348
r_mcangle_it6.576
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.925
r_dihedral_angle_3_deg14.561
r_dihedral_angle_2_deg12.972
r_lrange_other12.391
r_lrange_it12.388
r_scangle_other11.722
r_scangle_it11.719
r_scbond_it8.357
r_scbond_other8.348
r_mcangle_it6.576
r_mcangle_other6.575
r_dihedral_angle_1_deg5.491
r_mcbond_it5.376
r_mcbond_other5.365
r_angle_refined_deg2.03
r_angle_other_deg0.905
r_nbd_refined0.205
r_symmetry_xyhbond_nbd_refined0.172
r_nbtor_refined0.16
r_xyhbond_nbd_refined0.139
r_symmetry_nbd_other0.129
r_chiral_restr0.113
r_symmetry_nbd_refined0.11
r_nbd_other0.066
r_symmetry_nbtor_other0.062
r_bond_refined_d0.014
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 Atoms2190
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing