X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 294.0
Details 25% PEG 4000 0.1 M MES pH 5.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.49 α = 84.82
b = 80.09 β = 82.33
c = 88.69 γ = 82.24
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2018-03-25
Diffraction Radiation
Monochromator Protocol
SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3 50 89.1 0.092 -- -- 1.9 -- 30469 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.0 3.05 90.7 0.442 -- -- 1.9 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.0 39.6 -- -- -- 28977 1492 88.9 -- 0.217 0.214 0.274 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.0 3.08 -- 104 2144 0.327 0.329 -- 87.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.95
Anisotropic B[1][1] 1.84
Anisotropic B[1][2] 1.48
Anisotropic B[1][3] -3.11
Anisotropic B[2][2] -0.25
Anisotropic B[2][3] -1.24
Anisotropic B[3][3] -2.01
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.184
r_dihedral_angle_1_deg 6.981
r_mcbond_other 2.528
r_angle_refined_deg 1.451
r_chiral_restr 0.053
r_bond_other_d 0.001
r_scbond_it 2.688
r_bond_refined_d 0.006
r_mcangle_other 4.161
r_dihedral_angle_2_deg 35.977
r_long_range_B_other 9.892
r_dihedral_angle_3_deg 18.934
r_scangle_other 4.509
r_long_range_B_refined 9.891
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_scbond_other 2.689
r_mcbond_it 2.528
r_dihedral_angle_4_deg 17.044
r_mcangle_it 4.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12342
Nucleic Acid Atoms 0
Heterogen Atoms 362
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0232
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing