X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.2
Temperature 293.0
Details ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.3 α = 90
b = 102.3 β = 90
c = 112.3 γ = 120
Symmetry
Space Group P 6 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU mirrors 1998-11-18
Diffraction Radiation
Monochromator Protocol
DOUBLE-CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.708 SPRING-8 BL44B2

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
2.5 50 91.7 0.069 -- -- 14.4 12434 11480 0.0 0.0 --
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)
2.5 2.59 55.2 -- 0.304 -- -- --

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 2.5 15.3 0.0 0.0 12488 10491 1085 84.0 -- 0.224 0.224 0.271 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 2.5 2.59 359 41 -- 0.288 0.342 -- --
X Ray Diffraction 2.69 2.81 951 100 -- 0.273 0.337 -- --
X Ray Diffraction 2.96 3.15 1192 124 -- 0.227 0.293 -- --
X Ray Diffraction 3.39 3.72 1223 122 -- 0.21 0.29 -- --
X Ray Diffraction 4.25 5.32 1267 129 -- 0.212 0.225 -- --
X Ray Diffraction 5.32 15.3 1328 144 -- 0.245 0.273 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 47.0
Anisotropic B[1][1] -1.38
Anisotropic B[1][2] -3.256
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.761
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.775
c_dihedral_angle_d 18.103
c_angle_deg 1.194
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 8.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1750
Nucleic Acid Atoms 0
Heterogen Atoms 298
Solvent Atoms 25

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
SCALA data reduction
MOSFLM data collection