X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.4
Details PROTEIN WAS CRYSTALLIZED USING MICRO BATCH METHOD UNDER OIL FROM 27.5% PEG 4000, 10% DIOXANE AND 100 MM, TRIS/HCL(PH 8.4).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.32 α = 90
b = 78.54 β = 90
c = 86.04 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 RAXIS V RIGAKU CYLINDRICAL BEND MIRROR 2002-10-15
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45XU -- 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
1.65 50 99.5 0.064 -- -- 4.4 -- 174516 -- -0.5 15.4
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)
1.65 1.71 99.5 0.383 -- 2.4 -- --

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 1.65 43.02 -- 0.0 -- 38745 1938 98.3 -- 0.213 0.213 0.239 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 1.65 1.75 -- 316 5930 0.289 0.321 0.018 96.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 22.7
Anisotropic B[1][1] 2.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.76
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.005
c_angle_deg 1.2
c_mcbond_it 2.68
c_scbond_it 4.18
c_scangle_it 5.88
c_improper_angle_d 0.85
c_mcangle_it 3.62
c_dihedral_angle_d 23.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2731
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 332

Software

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