5LAF

Room temperature X-ray diffraction of tetragonal HEWL with 1M of uridine. First data set (0.31 MGy)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.7291protein: 50 mg/ml of HEWL in mQ crystallization solution: 200mM NaAcetate pH 4.7 + 10% NaCl
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.11α = 90
b = 79.11β = 90
c = 37.897γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9840019ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.539.5699.80.040.99826.66.41978713.791
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.80.3125.66.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1BWH1.539.561881093799.690.145720.14420.17636RANDOM20.736
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]
-0.1-0.10.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.223
r_dihedral_angle_4_deg23.281
r_dihedral_angle_3_deg16.13
r_long_range_B_other7.979
r_long_range_B_refined7.974
r_scangle_other6.556
r_dihedral_angle_1_deg5.957
r_scbond_it4.195
r_scbond_other4.192
r_mcangle_other2.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.223
r_dihedral_angle_4_deg23.281
r_dihedral_angle_3_deg16.13
r_long_range_B_other7.979
r_long_range_B_refined7.974
r_scangle_other6.556
r_dihedral_angle_1_deg5.957
r_scbond_it4.195
r_scbond_other4.192
r_mcangle_other2.986
r_mcangle_it2.963
r_angle_refined_deg2.329
r_mcbond_it2.149
r_mcbond_other1.92
r_angle_other_deg1.193
r_chiral_restr0.149
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1001
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing