X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 296.0
Details MPD, MgCl2, NaCl, pH 6.5, vapor diffusion, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.99 α = 90
b = 29.99 β = 90
c = 119.07 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-02-08
Diffraction Radiation
Monochromator Protocol
Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9763 ESRF ID29

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
2.29 39.69 96.3 0.051 0.051 -- 4.9 -- 3006 -- -3.0 47.698
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)
2.29 2.43 85.1 0.112 -- 6.5 -- --

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 2.31 39.69 -- -- -- 2719 289 97.73 -- 0.2552 0.2521 0.2833 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 2.305 2.365 -- 24 168 0.79 0.974 -- 87.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.9258
Anisotropic B[1][1] -22.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -22.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 44.54
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.387
r_scbond_it 1.469
r_mcangle_it 1.129
r_mcbond_it 0.495
r_gen_planes_refined 0.007
r_chiral_restr 0.063
r_angle_refined_deg 2.403
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 450
Heterogen Atoms 26
Solvent Atoms 5

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
MOLREP molecular replacement
Xscale data processing