X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM MES/Tris, 2.5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.12 α = 90
b = 102.31 β = 90
c = 52.88 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-10-07
Diffraction Radiation
Monochromator Protocol
Si(111) 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
2.04 30 97.3 0.07 -- -- 4.9 -- n/a 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)
2.04 2.08 80.9 0.333 -- 5.1 2.2 1401

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 2.049 29.735 -- 1.33 -- 35101 1760 99.66 -- 0.2196 0.2181 0.2503 --
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 2.0495 2.1049 -- 131 2467 0.3713 0.4169 -- 98.0
X Ray Diffraction 2.1049 2.1668 -- 132 2509 0.3643 0.3878 -- 99.0
X Ray Diffraction 2.1668 2.2367 -- 135 2523 0.3481 0.3572 -- 99.0
X Ray Diffraction 2.2367 2.3166 -- 129 2527 0.339 0.4182 -- 100.0
X Ray Diffraction 2.3166 2.4093 -- 135 2557 0.286 0.3744 -- 100.0
X Ray Diffraction 2.4093 2.5189 -- 132 2551 0.2716 0.3352 -- 100.0
X Ray Diffraction 2.5189 2.6516 -- 137 2538 0.2426 0.2747 -- 100.0
X Ray Diffraction 2.6516 2.8177 -- 136 2557 0.2271 0.2639 -- 100.0
X Ray Diffraction 2.8177 3.035 -- 133 2551 0.2085 0.2561 -- 100.0
X Ray Diffraction 3.035 3.3401 -- 137 2597 0.202 0.2273 -- 100.0
X Ray Diffraction 3.3401 3.8225 -- 138 2587 0.1918 0.237 -- 100.0
X Ray Diffraction 3.8225 4.8127 -- 142 2630 0.1717 0.2088 -- 100.0
X Ray Diffraction 4.8127 29.7385 -- 143 2747 0.1968 0.188 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 12.7286
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.7188
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.0098
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.072
f_dihedral_angle_d 18.268
f_angle_d 1.323
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2738
Nucleic Acid Atoms 651
Heterogen Atoms 32
Solvent Atoms 186

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER in PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER version: in PHENIX model building
CBASS data collection