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 Molecular Dimensions Morpheus screen g50: 10% PEG 8000, 20% ethylene glycol; 20mM of each Na-formate, Ammonium-acetate, Na3-citrate, NaK D/L tartrate, Na-oxamate; 100mM MOPS/HEPES pH 7.5; INVAN.07057.A.D15.PD909136 AT 20.45MG/ML, direct cryo, vapor diffusion, sitting drop, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.8 α = 90
b = 68.8 β = 90
c = 395.65 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-12-12
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.9 50 99.0 0.072 -- -- 8.9 45568 45117 0.0 -3.0 35.36
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)
1.9 1.95 100.0 0.52 -- 4.54 -- --

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 1.9 47.6 -- 0.0 45568 45103 2279 99.36 0.1751 0.1751 0.1737 0.2014 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 1.9 1.949 -- 169 3084 0.212 0.272 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic, TLS
Mean Isotropic B 37.196
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.16
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.164
r_mcbond_other 1.373
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.334
r_angle_other_deg 0.763
r_dihedral_angle_1_deg 6.035
r_dihedral_angle_2_deg 37.517
r_dihedral_angle_3_deg 12.199
r_dihedral_angle_4_deg 15.644
r_chiral_restr 0.075
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_mcbond_it 1.374
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3195
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 255

Software

Computing
Computing Package Purpose
LS-CAT software 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