X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 296.0
Details Peg3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.32 α = 90
b = 56.61 β = 102.04
c = 93.14 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-09-14
Diffraction Radiation
Monochromator Protocol
Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
2.72 27.19 90.08 -- -- -- -- -- 25030 1.0 1.0 --
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)
2.7226 2.7907 66.0 -- -- -- -- --

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 2.723 27.195 -- 0.09 -- 25030 2008 90.08 0.24 0.2248 0.2182 0.292 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 2.7226 2.7907 -- 102 1202 0.3514 0.4549 -- 66.0
X Ray Diffraction 2.7907 2.866 -- 126 1426 0.3488 0.3993 -- 78.0
X Ray Diffraction 2.866 2.9503 -- 142 1403 0.3267 0.4363 -- 79.0
X Ray Diffraction 2.9503 3.0454 -- 125 1466 0.3102 0.3776 -- 82.0
X Ray Diffraction 3.0454 3.1541 -- 138 1563 0.282 0.3729 -- 87.0
X Ray Diffraction 3.1541 3.2801 -- 138 1673 0.2643 0.327 -- 91.0
X Ray Diffraction 3.2801 3.4292 -- 146 1655 0.2623 0.3475 -- 92.0
X Ray Diffraction 3.4292 3.6096 -- 144 1747 0.2587 0.3828 -- 95.0
X Ray Diffraction 3.6096 3.8351 -- 160 1753 0.2244 0.3205 -- 97.0
X Ray Diffraction 3.8351 4.1303 -- 151 1763 0.1834 0.299 -- 96.0
X Ray Diffraction 4.1303 4.5442 -- 156 1815 0.1614 0.2436 -- 99.0
X Ray Diffraction 4.5442 5.1978 -- 157 1824 0.1708 0.2482 -- 98.0
X Ray Diffraction 5.1978 6.5337 -- 155 1817 0.2073 0.2825 -- 99.0
X Ray Diffraction 6.5337 27.1959 -- 168 1915 0.1994 0.2587 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -10.8835
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.5565
Anisotropic B[2][2] -13.1072
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 23.9908
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.096
f_dihedral_angle_d 21.693
f_angle_d 1.479
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5248
Nucleic Acid Atoms 624
Heterogen Atoms 63
Solvent Atoms 41

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
Phaser model building
CBASS data collection