X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 30 % PEG 5K MME 0.2 M Ammonium sulfate 0.1 M MES pH 6.5 1 mM Mecbecin 4 mM MgCl2 2 mM TCEP ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.88 α = 90
b = 96.88 β = 90
c = 159.7 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-09-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
2.81 40 99.9 0.139 -- -- 7.6 19287 19268 0.0 0.0 75.9
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)
2.81 2.91 99.4 0.991 -- 2.0 5.7 1868

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 2.81 39.92 -- 0.0 19236 19044 974 99.0 0.2414 0.2414 0.2394 0.2793 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 2.808 2.881 1281 70 2552 0.2711 0.3028 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.3994
Anisotropic B[1][1] -1.0799
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0799
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.1599
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.009
t_other_torsion 18.1
t_omega_torsion 2.31
t_angle_deg 1.07
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4016
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
BUSTER-TNT refinement
PDB_EXTRACT data extraction version: 3.10
HKL-3000 data collection
BUSTER refinement version: 2.8.0