X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 291.0
Details 50mM imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.8 α = 90
b = 79.26 β = 105.62
c = 54.37 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 RIGAKU SATURN 92 mirrors 2011-04-21
Diffraction Radiation
Monochromator Protocol
mirrors Varimax HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
1.95 50 98.3 0.114 -- -- 4.7 -- n/a 0.0 -3.0 22.2
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)
1.95 2.02 86.3 0.5 -- 2.29 3.4 2802

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 1.949 22.097 -- 0.0 29554 29554 2930 90.29 0.2083 0.2083 0.2026 0.2589 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 1.9488 1.9808 -- 103 884 0.2447 0.2835 -- 64.0
X Ray Diffraction 1.9808 2.0149 -- 127 1118 0.214 0.2804 -- 80.0
X Ray Diffraction 2.0149 2.0515 -- 141 1279 0.2133 0.3007 -- 92.0
X Ray Diffraction 2.0515 2.091 -- 146 1378 0.2125 0.2689 -- 98.0
X Ray Diffraction 2.091 2.1336 -- 148 1367 0.1978 0.304 -- 98.0
X Ray Diffraction 2.1336 2.18 -- 153 1371 0.2005 0.2566 -- 98.0
X Ray Diffraction 2.18 2.2306 -- 148 1327 0.2018 0.2885 -- 96.0
X Ray Diffraction 2.2306 2.2863 -- 152 1352 0.1994 0.2646 -- 95.0
X Ray Diffraction 2.2863 2.3481 -- 134 1262 0.2035 0.3061 -- 90.0
X Ray Diffraction 2.3481 2.4171 -- 136 1245 0.2103 0.304 -- 90.0
X Ray Diffraction 2.4171 2.495 -- 129 1189 0.2399 0.2827 -- 84.0
X Ray Diffraction 2.495 2.5841 -- 126 1194 0.2369 0.2876 -- 85.0
X Ray Diffraction 2.5841 2.6874 -- 140 1147 0.2457 0.3604 -- 84.0
X Ray Diffraction 2.6874 2.8094 -- 130 1148 0.2457 0.3136 -- 82.0
X Ray Diffraction 2.8094 2.9572 -- 120 1129 0.2416 0.3016 -- 81.0
X Ray Diffraction 2.9572 3.142 -- 116 1285 0.2227 0.3404 -- 89.0
X Ray Diffraction 3.142 3.3838 -- 155 1409 0.2083 0.2395 -- 100.0
X Ray Diffraction 3.3838 3.7229 -- 171 1395 0.2089 0.2589 -- 100.0
X Ray Diffraction 3.7229 4.2583 -- 153 1331 0.1598 0.1871 -- 95.0
X Ray Diffraction 4.2583 5.3524 -- 157 1374 0.1614 0.2028 -- 96.0
X Ray Diffraction 5.3524 22.0984 -- 145 1440 0.1805 0.2125 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 22.2
Anisotropic B[1][1] -2.3841
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.6468
Anisotropic B[2][2] 0.787
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5971
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 20.555
f_angle_d 1.123
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2620
Nucleic Acid Atoms 632
Heterogen Atoms 4
Solvent Atoms 360

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CNS model building
StructureStudio data collection