X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 296.0
Details 80-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.26 α = 90
b = 98.48 β = 105.26
c = 93.02 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2013-11-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 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
2.5 89.74 100.0 0.084 -- -- 4.2 -- 54486 -- -- 48.2
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)
2.5 2.57 99.9 0.938 -- 1.6 4.2 --

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
FOURIER SYNTHESIS 2.5 89.74 -- -- -- 51674 2735 99.82 -- 0.19112 0.18905 0.2299 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 2.5 2.565 -- 214 3778 0.337 0.354 -- 99.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.615
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 34.186
r_long_range_B_other 6.14
r_gen_planes_refined 0.008
r_dihedral_angle_4_deg 12.114
r_chiral_restr 0.096
r_dihedral_angle_3_deg 15.153
r_angle_refined_deg 1.545
r_bond_other_d 0.008
r_long_range_B_refined 6.146
r_scangle_other 4.192
r_mcangle_it 3.25
r_bond_refined_d 0.014
r_angle_other_deg 1.802
r_gen_planes_other 0.006
r_scbond_it 2.628
r_mcangle_other 3.249
r_mcbond_it 2.065
r_mcbond_other 2.065
r_scbond_other 2.627
r_dihedral_angle_1_deg 5.541
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9683
Nucleic Acid Atoms 0
Heterogen Atoms 255
Solvent Atoms 367

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
iMOSFLM data reduction version: 0.1.27
Aimless data scaling version: 0.3.11
Coot model building version: 0.7.2
REFMAC phasing