X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.7
Temperature 277.0
Details PEG 4000, Tris.HCl, sodium acetate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 209.05 α = 90
b = 313.96 β = 90
c = 162.03 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH 58 cm long, Pt-coated, fused silica, vertical focus mirror 2002-03-25
Diffraction Radiation
Monochromator Protocol
Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1

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
2.4 20 95.7 -- 0.058 -- 4.16 197708 197708 0.0 0.0 34.7
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)
2.4 2.49 87.7 -- 0.3 4.1 3.83 18004

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 2.4 19.99 -- 0.0 206112 197455 9679 95.8 -- -- 0.195 0.215 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 2.4 2.49 18069 884 17185 0.263 0.292 0.01 88.0
X Ray Diffraction 2.49 2.58 18332 877 17455 0.253 0.288 0.01 89.4
X Ray Diffraction 2.58 2.7 18786 916 17870 0.241 0.256 0.008 91.5
X Ray Diffraction 2.7 2.84 19440 917 18523 0.232 0.258 0.009 94.9
X Ray Diffraction 2.84 3.02 20070 1008 19062 0.227 0.251 0.008 97.7
X Ray Diffraction 3.02 3.25 20447 990 19457 0.23 0.247 0.008 99.4
X Ray Diffraction 3.25 3.58 20496 981 19515 0.216 0.237 0.008 99.5
X Ray Diffraction 3.58 4.09 20478 1002 19476 0.187 0.211 0.007 99.1
X Ray Diffraction 4.09 5.14 20556 1032 19524 0.139 0.159 0.005 99.0
X Ray Diffraction 5.14 19.99 20781 1072 19709 0.152 0.164 0.005 98.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Unrestrained, grouped. ARG, LYS, GLU and GLN had 3 groups per residue.
Mean Isotropic B 37.91
Anisotropic B[1][1] -4.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.93
RMS Deviations
Key Refinement Restraint Deviation
c_torsion_impr_deg 0.79
c_torsion_deg 22.2
c_bond_d 0.006
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 20994
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 1618

Software

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing