X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 15% PEG8000, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.27 α = 71.9
b = 49.14 β = 81.58
c = 84.72 γ = 70.26
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-11-22
Diffraction Radiation
Monochromator Protocol
sagitally focused Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9795 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
2.53 50 98.6 0.093 -- -- 2.2 22648 22331 0.0 -3.0 37.3
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)
2.528 2.62 97.9 0.315 -- -- 2.1 2242

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 2.528 44.505 -- 0.1 22331 21058 1027 92.32 0.253 0.231 0.2277 0.2939 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 2.528 2.6614 -- 127 2534 0.281 0.3862 -- 81.0
X Ray Diffraction 2.6614 2.8281 -- 137 2715 0.2674 0.3397 -- 87.0
X Ray Diffraction 2.8281 3.0464 -- 152 2749 0.2513 0.3529 -- 90.0
X Ray Diffraction 3.0464 3.3529 -- 149 2937 0.2438 0.3239 -- 94.0
X Ray Diffraction 3.3529 3.8378 -- 152 3017 0.2165 0.295 -- 98.0
X Ray Diffraction 3.8378 4.8343 -- 170 3001 0.1911 0.2322 -- 98.0
X Ray Diffraction 4.8343 44.5122 -- 140 3078 0.2045 0.2447 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 29.0633
Anisotropic B[1][1] 14.9303
Anisotropic B[1][2] -3.4691
Anisotropic B[1][3] 5.3177
Anisotropic B[2][2] -6.2206
Anisotropic B[2][3] 0.0399
Anisotropic B[3][3] -8.7097
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.045
f_bond_d 0.003
f_angle_d 0.631
f_plane_restr 0.003
f_dihedral_angle_d 18.754
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 50.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5078
Nucleic Acid Atoms 0
Heterogen Atoms 136
Solvent Atoms 163

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
PHASER phasing