X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.68 α = 90
b = 119.07 β = 90
c = 155.08 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
CCD SBC-2 VERTICAL FOCUSING MIRROR 2000-07-02
Diffraction Radiation
Monochromator Protocol
ROSENBAUM-ROCK MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-ID

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
2.62 20 98.4 0.058 0.058 -- 6.7 21406 21406 0.0 -3.0 78.4
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)
2.62 2.71 91.6 0.312 0.312 -- 5.2 1952

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 2.62 19.84 0.0 2.0 21653 21084 1499 97.4 0.239 0.236 0.233 0.277 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 2.62 2.74 -- 177 2387 0.36 0.353 0.027 90.1
X Ray Diffraction 2.74 2.88 -- 192 2572 0.333 0.329 0.024 96.1
X Ray Diffraction 2.88 3.06 -- 173 2622 0.283 0.281 0.021 97.8
X Ray Diffraction 3.06 3.3 -- 193 2627 0.294 0.295 0.021 98.3
X Ray Diffraction 3.3 3.63 -- 178 2667 0.252 0.255 0.019 99.0
X Ray Diffraction 3.63 4.15 -- 186 2697 0.222 0.225 0.016 99.4
X Ray Diffraction 4.15 5.21 -- 201 2719 0.179 0.179 0.013 99.7
X Ray Diffraction 5.21 19.84 -- 199 2793 0.208 0.207 0.015 98.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 61.53
Anisotropic B[1][1] -16.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 21.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.36
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_improper_angle_d 1.1
c_angle_deg 1.3
c_dihedral_angle_d 20.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.42
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3002
Nucleic Acid Atoms 732
Heterogen Atoms 0
Solvent Atoms 9

Software

Software
Software Name Purpose
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing