X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details 0.17M Sodium Acetate, 0.085M Tris-HCl, pH 8.5, 25.5% PEG-4000, 15% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 141.22 α = 90
b = 30.61 β = 122.45
c = 89.82 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-03-23
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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 50 98.8 0.056 -- -- 3.1 -- 22172 -- -- --
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)
2.0 2.03 90.3 0.348 -- -- 2.7 1010

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 2.0 37.98 -- 0.0 -- 22156 1128 98.9 -- 0.1822 0.1809 0.2066 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 2.001 2.053 -- 78 1421 0.215 0.273 -- 92.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.1093
Anisotropic B[1][1] 24.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 8.81
Anisotropic B[2][2] -11.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -13.44
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.125
r_mcangle_it 2.267
r_mcbond_it 1.478
r_gen_planes_refined 0.008
r_chiral_restr 0.089
r_dihedral_angle_4_deg 16.985
r_dihedral_angle_3_deg 14.045
r_dihedral_angle_2_deg 36.77
r_dihedral_angle_1_deg 6.194
r_angle_refined_deg 1.162
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 1261
Heterogen Atoms 3
Solvent Atoms 220

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK 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: 2.3.0 molecular replacement
SCALEPACK data reduction