X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details 0.2M Sodium malonate, 20% PEG3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.92 α = 90
b = 64.52 β = 90
c = 82.84 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 315r -- 2010-07-30
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 -- Australian Synchrotron MX2

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
1.25 42.92 99.2 0.071 0.071 -- 5.5 63800 63800 0.0 -4.0 8.3
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)
1.25 1.32 99.4 0.401 0.401 3.7 5.5 9225

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 1.25 41.421 0.0 1.35 63749 63749 3231 99.0 -- 0.1487 0.1476 0.1696 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 1.25 1.2947 -- 297 6018 0.2215 0.252 -- 99.0
X Ray Diffraction 1.2947 1.3465 -- 340 5964 0.1757 0.1988 -- 99.0
X Ray Diffraction 1.3465 1.4078 -- 337 6007 0.1473 0.1986 -- 100.0
X Ray Diffraction 1.4078 1.482 -- 331 6030 0.124 0.1602 -- 100.0
X Ray Diffraction 1.482 1.5749 -- 304 6081 0.1105 0.1434 -- 100.0
X Ray Diffraction 1.5749 1.6965 -- 342 6054 0.1146 0.1537 -- 100.0
X Ray Diffraction 1.6965 1.8672 -- 330 6081 0.1272 0.1569 -- 100.0
X Ray Diffraction 1.8672 2.1374 -- 315 6072 0.143 0.177 -- 99.0
X Ray Diffraction 2.1374 2.6928 -- 314 6082 0.1494 0.1604 -- 98.0
X Ray Diffraction 2.6928 41.444 -- 321 6129 0.1628 0.1668 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Anisotropic B[1][1] -3.3034
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.8542
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4492
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_bond_d 0.011
f_angle_d 1.372
f_dihedral_angle_d 12.873
f_chiral_restr 0.09
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1840
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 421

Software

Software
Software Name Purpose
Blu-Ice data collection version: ICE
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_928)
MOSFLM data reduction
SCALA data scaling