X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.2
Temperature 293.0
Details 0.2 M Na2HPO4/KH2PO4, 2.5 M Sodium Chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.18 α = 90
b = 117.18 β = 90
c = 186.62 γ = 90
Symmetry
Space Group P 43 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-04-27
Diffraction Radiation
Monochromator Protocol
ROSENBAUM-ROCK DOUBLE CRYSTAL 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
2.7 50 99.9 0.091 0.063 -- 5.3 68317 40725 1.0 1.0 59.83
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)
2.7 2.75 100.0 0.89 -- -- 5.3 3433

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 2.7 45.691 -- 1.35 40725 36353 1821 99.77 -- 0.1782 0.176 0.219 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 2.7001 2.7731 -- 136 2598 0.2443 0.2907 -- 100.0
X Ray Diffraction 2.7731 2.8547 -- 131 2631 0.2586 0.2816 -- 100.0
X Ray Diffraction 2.8547 2.9468 -- 143 2599 0.2484 0.3236 -- 100.0
X Ray Diffraction 2.9468 3.0521 -- 112 2632 0.2351 0.2727 -- 100.0
X Ray Diffraction 3.0521 3.1742 -- 143 2623 0.2246 0.3076 -- 100.0
X Ray Diffraction 3.1742 3.3187 -- 142 2636 0.2147 0.2717 -- 100.0
X Ray Diffraction 3.3187 3.4936 -- 151 2615 0.1947 0.2279 -- 100.0
X Ray Diffraction 3.4936 3.7124 -- 130 2637 0.1813 0.2152 -- 100.0
X Ray Diffraction 3.7124 3.9989 -- 150 2656 0.1628 0.2254 -- 100.0
X Ray Diffraction 3.9989 4.401 -- 133 2658 0.1402 0.197 -- 100.0
X Ray Diffraction 4.401 5.0371 -- 152 2671 0.1289 0.1638 -- 100.0
X Ray Diffraction 5.0371 6.3435 -- 143 2724 0.1601 0.186 -- 100.0
X Ray Diffraction 6.3435 45.6976 -- 155 2852 0.1678 0.2003 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.7633
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.908
f_plane_restr 0.007
f_chiral_restr 0.081
f_angle_d 1.383
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6154
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 96

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-3000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
MOLREP molecular replacement
SCALEPACK data reduction