8Q3L | pdb_00008q3l

Human Gamma-D Crystallin R36S fresh serial crystallographic structure


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HK0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.829850 mM phosphate buffer pH 7.8, 20 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.5852.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.6α = 90
b = 83.7β = 90
c = 100.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M2021-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.99DiamondI24

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
12.138.6699.90.9740.193.8726.750856
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)
12.12.140.491.640.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.138.6625669131799.670.206240.20370.210.257830.26RANDOM37.965
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]
-0.64-0.070.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.42
r_dihedral_angle_2_deg14.232
r_long_range_B_other11.283
r_long_range_B_refined11.28
r_scangle_other7.897
r_dihedral_angle_1_deg6.899
r_scbond_it5.046
r_scbond_other5.044
r_mcangle_other4.481
r_mcangle_it4.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.42
r_dihedral_angle_2_deg14.232
r_long_range_B_other11.283
r_long_range_B_refined11.28
r_scangle_other7.897
r_dihedral_angle_1_deg6.899
r_scbond_it5.046
r_scbond_other5.044
r_mcangle_other4.481
r_mcangle_it4.48
r_mcbond_it3.041
r_mcbond_other3.034
r_angle_refined_deg1.45
r_angle_other_deg0.506
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms2887
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata scaling
CrystFELdata reduction
MOLREPphasing