X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 10% MPD, 40 mM Na Cacodylate (pH 7.0), 12mM Spermine Tetra-HCl, 80 mM Potassium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.1 α = 90
b = 47.1 β = 90
c = 424.65 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 1 -- 2010-08-01
Diffraction Radiation
Monochromator Protocol
Si(111) channel-cut crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.9795 NSLS X12C

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
2.2 50 99.8 0.5109 -- -- 18.8 9870 8288 0.0 0.0 --
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)
2.2 2.28 99.4 0.89 -- 3.3 10.7 959

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 2.3 30.0 -- -- 8288 8206 421 99.44 -- 0.2173 0.21484 0.26977 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 2.3 2.36 -- 29 606 0.306 0.279 -- 99.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.531
Anisotropic B[1][1] 2.01
Anisotropic B[1][2] 1.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.012
r_scbond_it 0.729
r_symmetry_hbond_refined 0.125
r_symmetry_vdw_refined 0.157
r_xyhbond_nbd_refined 0.12
r_nbtor_refined 0.262
r_nbd_refined 0.142
r_gen_planes_refined 0.004
r_chiral_restr 0.053
r_angle_refined_deg 1.169
r_bond_refined_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.174
Luzzati ESD (R-Free Set) 0.245
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1162
Heterogen Atoms 3
Solvent Atoms 71

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
PHASES model building
ADSC version: Quantum data collection