X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 290.0
Details EB JCSG screen a9: 200mM Ammonium chloride, 20% PEG 3350 PEG 1500; ButhA.00036.a.A1.PS01171 at 20 mg/ml, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.93 α = 90
b = 53.93 β = 90
c = 465.92 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-01-18
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.127092 SSRL BL7-1

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
1.85 50 97.2 0.071 -- -- 18.7 36489 35480 0.0 -3.0 22.932
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)
1.85 1.9 90.4 0.132 -- 19.34 -- --

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 1.85 43.39 -- 0.0 36489 35443 1246 97.69 0.1837 0.1837 0.1821 0.2141 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 1.85 1.898 2222 104 2222 0.174 0.247 -- 90.47
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 18.0096
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.22
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.72
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.434
r_mcbond_other 0.882
r_bond_refined_d 0.014
r_bond_other_d 0.001
r_angle_refined_deg 1.518
r_angle_other_deg 0.764
r_dihedral_angle_1_deg 5.677
r_dihedral_angle_2_deg 31.778
r_dihedral_angle_3_deg 11.25
r_dihedral_angle_4_deg 20.566
r_chiral_restr 0.089
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 0.888
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2710
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 361

Software

Computing
Computing Package Purpose
BluIce Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.2 molecular replacement
Xscale data reduction