X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 290.0
Details EmeraldBio JCSG+ screen h7: 25% PEG 3350, 200mM ammonium sulphate, 100mM BisTris pH 5.5; LemaA.01212.a.A1.P001468 at 20mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.58 α = 90
b = 65.66 β = 110.11
c = 77.65 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 ADSC QUANTUM 315r -- 2012-07-28
Diffraction Radiation
Monochromator Protocol
Double-crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2

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
1.3 50 97.9 0.047 0.047 -- 9.7 -- 146529 0.0 -3.0 21.987
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)
1.3 1.33 94.0 0.336 -- 4.11 -- --

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 1.3 28.92 -- 0.0 149715 146506 7367 97.95 0.1534 0.1534 0.1522 0.1785 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 1.3 1.334 -- 533 9815 0.221 0.245 -- 93.99
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 21.4934
Anisotropic B[1][1] 0.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.57
Anisotropic B[2][2] -0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.47
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.372
r_dihedral_angle_2_deg 32.581
r_dihedral_angle_3_deg 11.217
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_bond_refined_d 0.013
r_dihedral_angle_4_deg 15.204
r_chiral_restr 0.102
r_angle_other_deg 0.847
r_angle_refined_deg 1.656
r_gen_planes_refined 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4438
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 635

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
BOS data collection
XDS data reduction