7RGR

Lysozyme 056 from Deep neural language modeling


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.52930.1 M CHES 9.5 pH, 30 %w/v PEG 3K
Crystal Properties
Matthews coefficientSolvent content
2.5952.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.15α = 90
b = 68.1β = 90
c = 95.41γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray92.5PIXELDECTRIS PILATUS3 6MPt/Rh mirrors2021-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11636ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.47555.4399.90.1330.1390.99913.7212.781475159.48
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)
12.4752.5499.60.7211.9611.97

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEtrRosetta prediction2.4855.431.921474076299.810.26080.25890.296464.89
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.0504
f_angle_d0.6324
f_chiral_restr0.0464
f_bond_d0.0039
f_plane_restr0.0037
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2664
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms14

Software

Software
Software NamePurpose
PHENIXrefinement
BUCCANEERmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing