X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.85
Temperature 295.0
Details MPD, MES, NaOH, pH 5.85, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.49 α = 90
b = 127.07 β = 90
c = 146.39 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V MIRRORS 2004-10-16
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1

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 40 99.8 0.099 -- -- 5.4 131899 131809 0.0 0.0 14.0
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)
1.8 1.87 96.9 0.456 -- 4.3 5.5 12123

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 39.14 0.0 0.0 131899 131809 6585 99.5 -- -- 0.2235 0.2584 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 1.87 12918 599 -- 0.268 0.315 0.013 98.3
X Ray Diffraction 1.87 1.94 13061 625 -- 0.25 0.275 0.011 99.7
X Ray Diffraction 1.94 2.03 13099 659 -- 0.241 0.285 0.011 99.7
X Ray Diffraction 2.03 2.14 13112 666 -- 0.238 0.266 0.01 99.7
X Ray Diffraction 2.14 2.27 13135 633 -- 0.22 0.255 0.01 99.8
X Ray Diffraction 2.27 2.44 13166 653 -- 0.22 0.259 0.01 99.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model OVERALL
Mean Isotropic B 20.5
Anisotropic B[1][1] -2.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.56
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 21.7
x_improper_angle_d 0.81
x_bond_d 0.006
x_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12180
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 1548

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CNS refinement version: 1.1
HKL-2000 data reduction
CNS phasing version: 1.1