X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 30% PEG 6000, 0.1M HEPES, 0.1M MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.73 α = 90
b = 121.12 β = 101.4
c = 106.65 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRRORS 2012-10-16
Diffraction Radiation
Monochromator Protocol
Si III SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.979 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
2.8 104.55 99.1 0.105 -- -- 9.7 37449 37449 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)
2.8 2.8 98.7 0.5 -- 1.0 8.8 3663

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
SAD 2.8 104.55 -- 0.0 35562 35562 1865 98.9 -- 0.208 0.204 0.291 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 2.802 2.874 -- 117 2492 0.281 0.404 -- 96.31
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.009
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.33
Anisotropic B[2][2] 2.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.03
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_chiral_restr 0.116
r_dihedral_angle_4_deg 18.914
r_dihedral_angle_3_deg 22.52
r_dihedral_angle_2_deg 36.074
r_dihedral_angle_1_deg 7.272
r_angle_refined_deg 1.736
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9638
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 156

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHELXD, SHELXE and ARP/wARP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
ARP/wARP model building
SHELXE model building
SHELXD model building
CBASS data collection