X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HPLPDB entry 1HPL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293200 mM magnesium acetate, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.8757.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.948α = 90
b = 153.206β = 90
c = 95.783γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray125PIXELDECTRIS PILATUS3 6MBe CRL/Si elliptical mirror2017-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B1.000ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.895.899.40.010.98513.53.337662
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.999.70.530.7281.53.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1HPL2.848.4135568183399.230.197380.195340.23545RANDOM94.934
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]
1.49-3.011.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.007
r_dihedral_angle_4_deg18.563
r_dihedral_angle_3_deg18.225
r_dihedral_angle_1_deg8.572
r_long_range_B_refined7.556
r_long_range_B_other7.556
r_scangle_other3.567
r_mcangle_it2.967
r_mcangle_other2.967
r_scbond_it2.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.007
r_dihedral_angle_4_deg18.563
r_dihedral_angle_3_deg18.225
r_dihedral_angle_1_deg8.572
r_long_range_B_refined7.556
r_long_range_B_other7.556
r_scangle_other3.567
r_mcangle_it2.967
r_mcangle_other2.967
r_scbond_it2.088
r_scbond_other2.088
r_mcbond_it1.763
r_mcbond_other1.762
r_angle_refined_deg1.433
r_angle_other_deg0.887
r_chiral_restr0.131
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms7873
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing