X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 25% PEG8000, 0.2 M NaCl, 0.1 M Hepes pH7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.62 α = 90
b = 68.75 β = 90
c = 102.88 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2015-06-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID

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
1.76 50.01 100.0 0.101 -- 25.746 9.2 -- 38381 -- -- --
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)
1.76 1.79 99.9 0.879 -- -- 6.5 1894

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 1.761 50.01 -- -- -- 37374 945 99.7 -- 0.17885 0.17761 0.22677 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 1.761 1.806 -- 65 2633 0.256 0.24 -- 96.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.803
Anisotropic B[1][1] -0.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.02
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_mcbond_it 1.381
r_scangle_other 2.979
r_bond_refined_d 0.01
r_gen_planes_refined 0.006
r_angle_other_deg 0.932
r_mcbond_other 1.379
r_scbond_other 1.844
r_long_range_B_other 5.03
r_long_range_B_refined 5.121
r_mcangle_it 2.224
r_scbond_it 1.845
r_dihedral_angle_4_deg 17.869
r_chiral_restr 0.093
r_angle_refined_deg 1.506
r_dihedral_angle_1_deg 6.318
r_bond_other_d 0.002
r_mcangle_other 2.224
r_dihedral_angle_2_deg 38.346
r_dihedral_angle_3_deg 11.987
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2935
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 306

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.15
MOLREP phasing
ARP model building