X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 10 MM MES PH 6.5, 10 MM ZINC SULFATE, 27.5% PEG550 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.14 α = 90
b = 104.14 β = 90
c = 44 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-07-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.99987 ESRF ID29

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
2.05 90 99.6 0.038 -- -- 14.6 -- 9222 -- 0.0 48.88
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)
2.05 2.1 99.9 0.593 -- 4.09 -- --

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
SAD 2.05 90.0 -- 0.0 -- 8762 460 99.6 -- 0.185 0.182 0.223 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 2.05 2.1 -- 35 629 0.279 0.323 -- 99.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 90.67
Anisotropic B[1][1] 0.7
Anisotropic B[1][2] 0.35
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.28
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.02
r_gen_planes_refined 0.012
r_angle_other_deg 0.971
r_dihedral_angle_3_deg 19.248
r_scangle_other 7.602
r_bond_other_d 0.001
r_chiral_restr 0.121
r_scbond_it 5.464
r_angle_refined_deg 2.169
r_dihedral_angle_1_deg 7.832
r_dihedral_angle_4_deg 25.563
r_gen_planes_other 0.001
r_mcbond_it 4.459
r_long_range_B_other 9.168
r_mcangle_other 5.661
r_mcbond_other 4.46
r_dihedral_angle_2_deg 41.937
r_long_range_B_refined 9.165
r_scbond_other 5.444
r_mcangle_it 5.663
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 870
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 28

Software

Software
Software Name Purpose
XDS data reduction
SCALA data scaling
Auto-Rickshaw phasing
REFMAC refinement version: 5.8.0073
Auto-Rickshaw phasing
Auto-Rickshaw phasing
Auto-Rickshaw phasing
Auto-Rickshaw phasing