6YP1

HiCel7B unliganded


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A39 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829812 mg/mL protein in 20 mM pH 8 Tris-HCl mixed 2:1 with 0.15 M sodium citrate, 0.8 M ammonium sulfate, 1 M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.4148.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.31α = 90
b = 92.31β = 90
c = 100.81γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (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
11.246.19899.80.05326.714135228
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2296.30.4833.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2A391.246.198135228679599.6830.1180.11670.135312.949
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]
0.3520.352-0.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.367
r_dihedral_angle_4_deg15.444
r_dihedral_angle_3_deg11.715
r_rigid_bond_restr8.186
r_dihedral_angle_1_deg6.763
r_scbond_other4.99
r_scbond_it4.989
r_scangle_it4.605
r_scangle_other4.604
r_lrange_it3.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.367
r_dihedral_angle_4_deg15.444
r_dihedral_angle_3_deg11.715
r_rigid_bond_restr8.186
r_dihedral_angle_1_deg6.763
r_scbond_other4.99
r_scbond_it4.989
r_scangle_it4.605
r_scangle_other4.604
r_lrange_it3.818
r_lrange_other3.632
r_angle_refined_deg2.32
r_angle_other_deg1.718
r_mcangle_it1.485
r_mcangle_other1.485
r_mcbond_it1.18
r_mcbond_other1.18
r_symmetry_nbd_refined0.326
r_symmetry_xyhbond_nbd_refined0.263
r_nbd_refined0.257
r_nbd_other0.23
r_symmetry_nbd_other0.211
r_xyhbond_nbd_refined0.206
r_nbtor_refined0.181
r_symmetry_xyhbond_nbd_other0.136
r_chiral_restr0.131
r_symmetry_nbtor_other0.098
r_bond_refined_d0.024
r_gen_planes_refined0.013
r_bond_other_d0.006
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3073
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing