X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 297.0
Details 0.2 M potassium chloride, 0.01 M magnesium chloride, 0.01 M DTT, 4.5% V/V PEG 8000, 1% V/V glycerol, 1% V/V MPD, 0.05 M MES buffer pH 5.6, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.11 α = 90
b = 163.6 β = 90
c = 109.33 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2000-04-07
Diffraction Radiation
Monochromator Protocol
DIAMOND THREE WAVELENGTH FROM GOLD DERIVATIVE
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 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
3 20 97.1 0.062 6.2 -- 3.173 66989 21113 0.0 0.0 45.1
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)
3.0 3.05 90.8 0.372 37.2 1.7 3.246 --

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
MAD 3.0 19.95 0.0 0.0 21111 21111 1038 95.8 -- -- 0.247 0.299 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 3.0 3.19 -- 150 3090 0.447 0.464 0.038 88.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 82.1
Anisotropic B[1][1] 29.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -15.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.66
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.1
c_scbond_it 20.26
c_mcangle_it 18.8
c_angle_deg 1.3
c_scangle_it 23.66
c_bond_d 0.007
c_mcbond_it 14.09
c_dihedral_angle_d 21.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Sigma A (Observed) 0.64
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.57
Luzzati Sigma A (R-Free Set) 0.64
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3126
Nucleic Acid Atoms 1060
Heterogen Atoms 3
Solvent Atoms 8

Software

Software
Software Name Purpose
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling
CNS phasing version: 0.9