X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4
Temperature 300.0
Details Protein: 7.5 mg/mL, 0.25 M sodium chloride, 0.01 M Tris-HCl, Crystal condition: PACT B1 (Qiagen), 0.1 M MIB buffer, 25% PEG1500, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.91 α = 90
b = 72.8 β = 90
c = 170.9 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 MARMOSAIC 300 mm CCD Beryllium lenses 2012-11-19
Diffraction Radiation
Monochromator Protocol
Diamond(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
1.8 30 99.3 0.11 -- -- 5.3 43485 43485 -- -3.0 --
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)
1.8 1.83 96.7 0.55 -- 2.8 4.2 2088

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 1.8 28.51 -- -- -- 41235 2183 99.2 -- 0.17956 0.17799 0.20823 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 1.8 1.847 -- 155 2903 0.242 0.284 -- 95.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.194
Anisotropic B[1][1] -0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.58
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.074
r_dihedral_angle_4_deg 12.622
r_dihedral_angle_3_deg 9.987
r_dihedral_angle_2_deg 36.182
r_dihedral_angle_1_deg 2.854
r_angle_other_deg 0.699
r_angle_refined_deg 1.256
r_bond_other_d 0.001
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3960
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 435

Software

Computing
Computing Package Purpose
Blu Max Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
PHASER model building
Blu version: Max data collection