X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 295.0
Details 8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 155.16 α = 90
b = 155.16 β = 90
c = 59.87 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-06-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C -- APS 24-ID-C

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
3.3 40 92.6 0.092 0.084 -- 2.7 21760 20444 -5.0 -5.0 63.6
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)
3.3 3.42 76.3 0.418 0.347 2.1 2.2 1644

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 3.3 40.0 -- 0.0 21760 18996 959 86.9 -- -- 0.251 0.305 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 3.3 3.36 686 35 651 0.404 0.524 -- --
X Ray Diffraction 3.36 3.42 751 43 708 0.343 0.45 -- --
X Ray Diffraction 3.42 3.49 841 54 787 0.323 0.324 -- --
X Ray Diffraction 3.49 3.57 896 48 848 0.315 0.412 -- --
X Ray Diffraction 3.57 3.65 954 52 902 0.355 0.396 -- --
X Ray Diffraction 3.65 3.74 988 57 931 0.312 0.442 -- --
X Ray Diffraction 3.74 3.85 1028 49 979 0.282 0.433 -- --
X Ray Diffraction 3.85 3.96 1054 46 1008 0.235 0.267 -- --
X Ray Diffraction 3.96 4.09 1028 52 976 0.237 0.291 -- --
X Ray Diffraction 4.09 4.23 1063 52 1011 0.234 0.295 -- --
X Ray Diffraction 4.23 4.4 1037 40 997 0.229 0.339 -- --
X Ray Diffraction 4.4 4.6 1096 64 1032 0.23 0.278 -- --
X Ray Diffraction 4.6 4.84 1076 45 1031 0.208 0.247 -- --
X Ray Diffraction 4.84 5.15 1093 57 1036 0.21 0.268 -- --
X Ray Diffraction 5.15 5.54 1082 52 1030 0.217 0.302 -- --
X Ray Diffraction 5.54 6.1 1074 43 1031 0.187 0.226 -- --
X Ray Diffraction 6.1 6.98 1072 53 1019 0.204 0.236 -- --
X Ray Diffraction 6.98 8.78 1088 56 1032 0.222 0.261 -- --
X Ray Diffraction 8.78 40.0 1089 61 1028 0.306 0.304 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 78.585
Anisotropic B[1][1] -10.926
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.926
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 21.851
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.636
c_mcbond_it 4.025
c_mcangle_it 6.842
c_scbond_it 3.972
c_bond_d 0.009
c_scangle_it 6.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5168
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 28

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
RESOLVE phasing version: 2.01
CNS refinement
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: Quantum
HKL-2000 data reduction