X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 298.0
Details 1.04M NaCitrate, MES pH 6.4, 5mM 2-mercaptoethanol, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 363.34 α = 90
b = 213.88 β = 125.2
c = 212.96 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-11-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1

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
3.3 30 97.0 0.071 -- -- 1.9 199279 193345 0.0 0.0 --
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)
3.3 3.42 96.8 0.658 -- 1.24 1.9 --

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 3.3 30.0 -- 1778.0 199279 191242 9560 96.0 -- 0.242 0.242 0.287 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 3.3 3.42 -- 932 -- 0.3795 0.3954 -- 89.02
X Ray Diffraction 3.42 3.55 -- 899 -- 0.3562 0.3913 -- 90.39
X Ray Diffraction 3.55 3.72 -- 960 -- 0.3247 0.3599 -- 91.18
X Ray Diffraction 3.72 3.91 -- 922 -- 0.2984 0.3367 -- 91.52
X Ray Diffraction 3.91 4.16 -- 1005 -- 0.2593 0.303 -- 91.57
X Ray Diffraction 4.16 4.48 -- 974 -- 0.2219 0.2715 -- 91.75
X Ray Diffraction 4.48 4.93 -- 965 -- 0.2152 0.2747 -- 91.96
X Ray Diffraction 4.93 5.64 -- 971 -- 0.2198 0.2842 -- 91.93
X Ray Diffraction 5.64 7.11 -- 929 -- 0.2278 0.2809 -- 92.16
X Ray Diffraction 7.11 30.0 -- 1003 -- 0.1904 0.2244 -- 90.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 120.6
Anisotropic B[1][1] -10.507
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 10.166
Anisotropic B[2][2] 17.115
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.608
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.95
c_dihedral_angle_d 23.34
c_bond_d 0.008687
c_angle_deg 1.42
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.49
Luzzati Sigma A (Observed) 0.85
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.57
Luzzati Sigma A (R-Free Set) 0.87
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 59299
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 0

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
CNS refinement version: 1.2
HKL-2000 data reduction
HKL-2000 data scaling