X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 290.0
Details 22% PEG2000, 50 mM sodium acetate, 90 mM magnesium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.63 α = 90
b = 61.82 β = 90
c = 69.6 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
CCD ADSC QUANTUM 315 -- 2010-02-10
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 1.1109 ALS 12.3.1

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
1.77 46.22 99.1 0.057 -- -- 7.0 -- 22178 -- -- --
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)
1.77 1.8 98.2 0.467 -- -- 7.2 --

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
FOURIER SYNTHESIS 1.769 46.222 -- 1.34 -- 22133 1112 98.98 -- 0.158 0.1561 0.1939 --
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 1.7691 1.8497 -- 133 2499 0.1768 0.2065 -- 97.0
X Ray Diffraction 1.8497 1.9472 -- 131 2592 0.1628 0.2328 -- 99.0
X Ray Diffraction 1.9472 2.0692 -- 124 2611 0.1472 0.2023 -- 98.0
X Ray Diffraction 2.0692 2.2289 -- 140 2599 0.1494 0.1853 -- 99.0
X Ray Diffraction 2.2289 2.4532 -- 138 2609 0.1469 0.2026 -- 99.0
X Ray Diffraction 2.4532 2.8082 -- 153 2627 0.1539 0.18 -- 100.0
X Ray Diffraction 2.8082 3.5378 -- 149 2680 0.1511 0.2002 -- 100.0
X Ray Diffraction 3.5378 46.2373 -- 144 2804 0.1634 0.1843 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.8617
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.9739
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.1122
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.01
f_chiral_restr 0.088
f_dihedral_angle_d 15.304
f_plane_restr 0.006
f_angle_d 1.292
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1833
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 234

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10
SERGUI data collection
HKL-2000 data reduction
HKL-2000 data scaling
REFMAC phasing