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_dihedral_angle_2_deg 31.778
r_bond_other_d 0.001
r_mcangle_it 1.434
r_bond_refined_d 0.014
r_mcbond_it 0.888
r_mcbond_other 0.882
r_gen_planes_other 0.001
r_angle_other_deg 0.764
r_dihedral_angle_3_deg 11.25
r_gen_planes_refined 0.007
r_chiral_restr 0.089
r_dihedral_angle_1_deg 5.677
r_angle_refined_deg 1.518
r_dihedral_angle_4_deg 20.566
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

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.2
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
XDS data reduction