X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 5.3
Temperature 295.0
Details PEG 4000, MAGNESIUM CHLORIDE, SODIUM CITRATE, pH 5.3, MICROBATCH, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.07 α = 90
b = 185.57 β = 90
c = 62.52 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V -- 2002-04-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.9 SPRING-8 BL45XU

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 30 97.7 0.095 -- -- 4.9 276295 276295 0.0 0.0 14.3
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)
2.0 2.07 81.1 0.235 -- 4.2 4.2 4619

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 2.0 30.0 -- 0.0 57573 56133 2850 97.5 -- -- 0.21 0.2576 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 2.0 2.09 -- 317 5800 0.283 0.32 0.018 86.2
X Ray Diffraction 2.09 2.2 -- 341 6594 0.248 0.288 0.016 97.8
X Ray Diffraction 2.2 2.34 -- 333 6711 0.2363 0.2818 0.015 98.6
X Ray Diffraction 2.34 2.52 -- 360 6727 0.2222 0.2752 0.015 99.3
X Ray Diffraction 2.52 2.77 -- 362 6759 0.2209 0.2727 0.014 99.4
X Ray Diffraction 2.77 3.17 -- 369 6772 0.2187 0.2668 0.014 99.2
X Ray Diffraction 3.17 4.0 -- 386 6824 0.1955 0.2597 0.013 99.2
X Ray Diffraction 4.0 30.0 -- 384 7121 0.1823 0.2174 0.011 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 28.4
Anisotropic B[1][1] 2.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.8
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6078
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 462

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS 1.1 Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 model building
HKL-2000 data collection
SCALEPACK data reduction
CNS version: 1.1 refinement