X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 293.0
Details NaCl, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.4 α = 90
b = 102.4 β = 90
c = 121.75 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1998-11-03
Diffraction Radiation
Monochromator Protocol
Ni Filter, Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
1.8 39.18 99.5 0.056 0.056 -- -- 67901 557664 0.0 0.0 21.7
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)
1.8 1.83 99.3 0.27 0.27 4.9 -- --

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 1.8 39.18 0.0 0.0 68228 67901 5434 99.5 0.2 0.2 0.197 0.217 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 1.8 1.86 5585 423 5162 0.283 0.293 0.014 98.9
X Ray Diffraction 1.86 1.92 5571 451 5120 0.242 0.268 0.013 99.1
X Ray Diffraction 1.92 1.99 5597 449 5148 0.211 0.236 0.011 99.2
X Ray Diffraction 1.99 2.07 5655 468 5187 0.197 0.221 0.01 99.7
X Ray Diffraction 2.07 2.16 5608 430 5178 0.196 0.212 0.01 99.7
X Ray Diffraction 2.16 2.27 5667 444 5223 0.196 0.211 0.01 99.6
X Ray Diffraction 2.27 2.42 5642 431 5211 0.201 0.23 0.011 99.8
X Ray Diffraction 2.42 2.6 5678 481 5197 0.206 0.228 0.01 99.8
X Ray Diffraction 2.6 2.86 5674 461 5213 0.202 0.214 0.01 99.9
X Ray Diffraction 2.86 3.28 5710 458 5252 0.198 0.21 0.01 99.8
X Ray Diffraction 3.28 4.13 5719 456 5263 0.172 0.198 0.009 99.1
X Ray Diffraction 4.13 39.18 5795 482 5313 0.192 0.21 0.01 97.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.65
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 1.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.99
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.2
x_torsion_deg 25.6
x_bond_d 0.005
x_torsion_impr_deg 0.62
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.12
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3516
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 447

Software

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