X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details THE TOC34 CRYSTALS WERE GROWN AT 4 DEGREES CELSIUS BY HANGING DROP VAPOR DIFFUSION. A 2-MICROLITER SOLUTION (10 MG/ML IN 50 MM TRIS-HCL AT PH 8.0 AND 0.1 M NACL) WAS MIXED WITH A 2-MICROLITER RESERVOIR SOLUTION CONTAINING 22% PEGMME 5K AND 10% GLYCEROL IN 0.1 M HEPES AT PH 6.5.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 143.16 α = 90
b = 78.67 β = 91.44
c = 67.28 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 1998-06-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 0.9796, 0.9794, 0.9680, 0.9802 PHOTON FACTORY BL-18B

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 31 99.0 0.056 -- -- 7.0 -- 50147 -- 2.0 6.5
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 2.1 98.8 0.223 -- 1.9 2.5 --

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 2.0 22.42 -- 2.0 -- 79906 7786 80.5 -- 0.186 0.186 0.23 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 2.13 -- 1010 8981 0.229 0.252 0.008 60.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.9
Anisotropic B[1][1] 7.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.7
Anisotropic B[2][2] -3.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.01
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.9
c_improper_angle_d 0.97
c_scangle_it 11.97
c_scbond_it 11.54
c_angle_deg 1.2
c_bond_d 0.009
c_mcangle_it 5.71
c_mcbond_it 3.68
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5890
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 670

Software

Computing
Computing Package Purpose
DPS, MOSFLM Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SOLVE model building