X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 292.0
Details Grid of PEG 3350 vs. MgCl2 with a buffer of Bis-TRIS at pH 6-6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.09 α = 86.05
b = 59.13 β = 74.92
c = 94.18 γ = 63.34
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2015-05-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

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
2.11 30 94.9 0.05 -- -- 2.0 -- 51361 -- -- --
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)
2.15 2.19 90.9 0.623 -- -- 1.8 --

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 2.1 29.47 -- -- -- 48761 2598 89.24 -- 0.24837 0.2475 0.26503 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 2.101 2.155 -- 43 672 0.297 0.351 -- 16.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 62.522
Anisotropic B[1][1] 40.14
Anisotropic B[1][2] -3.73
Anisotropic B[1][3] 7.61
Anisotropic B[2][2] -58.16
Anisotropic B[2][3] 11.19
Anisotropic B[3][3] 18.02
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_refined 3.854
r_gen_planes_refined 0.004
r_dihedral_angle_3_deg 13.893
r_mcbond_other 1.029
r_bond_refined_d 0.007
r_angle_other_deg 0.906
r_dihedral_angle_1_deg 4.836
r_chiral_restr 0.069
r_mcbond_it 1.029
r_mcangle_it 1.68
r_scbond_it 1.061
r_long_range_B_other 3.854
r_angle_refined_deg 1.158
r_dihedral_angle_4_deg 17.687
r_dihedral_angle_2_deg 34.364
r_mcangle_other 1.68
r_gen_planes_other 0.001
r_scbond_other 1.06
r_bond_other_d 0.002
r_scangle_other 1.677
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6963
Nucleic Acid Atoms 0
Heterogen Atoms 195
Solvent Atoms 45

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0155
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.24
HKL-2000 data reduction
PHASER phasing