X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 22% PEG3350, 0.2M Na Malonate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.63 α = 90
b = 67.38 β = 96.14
c = 105.89 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.972400 ESRF ID14-2

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
3.4 61.3 89.9 0.099 -- -- 2.8 12687 12318 2.0 2.0 --
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)
3.4 3.58 91.8 0.438 -- 2.4 2.8 1809

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 3.4 61.3 -- -- -- 11709 609 89.42 -- 0.28505 0.2819 0.34911 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 3.4 3.488 -- 48 843 0.35 0.405 -- 91.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 79.825
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.36
Anisotropic B[2][2] 0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.003
r_chiral_restr 0.048
r_dihedral_angle_4_deg 11.265
r_dihedral_angle_3_deg 14.624
r_dihedral_angle_2_deg 28.302
r_dihedral_angle_1_deg 3.272
r_angle_refined_deg 0.8
r_bond_refined_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6778
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DNA Data Collection
PROCESS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
molrep Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
molrep model building
DNA data collection