X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 298.0
Details 12% PEG 3350, 0.2M CaCl2, 0.1M MES, 3% glycerol, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.18 α = 90
b = 135.92 β = 90
c = 168.65 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 Bruker Platinum 135 Montel multilayer 2008-05-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.54 -- --

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
2.29 25 97.3 -- 0.123 -- 13.7 71501 69571 -- -- 31.4
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)
2.288 2.4 96.7 -- 0.476 4.8 11.2 8056

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 2.2881 24.972 -- 0.04 -- 69571 3513 97.33 -- 0.209 0.206 0.254 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 2.2881 2.3194 -- 108 2045 0.2668 0.3122 -- 77.0
X Ray Diffraction 2.3194 2.3525 -- 140 2595 0.2479 0.321 -- 96.0
X Ray Diffraction 2.3525 2.3876 -- 143 2543 0.239 0.3185 -- 96.0
X Ray Diffraction 2.3876 2.4249 -- 123 2618 0.2336 0.3356 -- 96.0
X Ray Diffraction 2.4249 2.4646 -- 130 2600 0.2321 0.2797 -- 97.0
X Ray Diffraction 2.4646 2.5071 -- 139 2580 0.2277 0.2758 -- 97.0
X Ray Diffraction 2.5071 2.5526 -- 148 2628 0.2383 0.3089 -- 98.0
X Ray Diffraction 2.5526 2.6017 -- 118 2641 0.2466 0.3012 -- 98.0
X Ray Diffraction 2.6017 2.6547 -- 152 2594 0.2403 0.3275 -- 98.0
X Ray Diffraction 2.6547 2.7124 -- 159 2647 0.2315 0.3076 -- 98.0
X Ray Diffraction 2.7124 2.7754 -- 151 2622 0.219 0.2963 -- 98.0
X Ray Diffraction 2.7754 2.8447 -- 127 2688 0.2214 0.2912 -- 99.0
X Ray Diffraction 2.8447 2.9215 -- 148 2633 0.2165 0.2732 -- 99.0
X Ray Diffraction 2.9215 3.0074 -- 131 2680 0.2194 0.2798 -- 99.0
X Ray Diffraction 3.0074 3.1043 -- 132 2715 0.2074 0.2535 -- 99.0
X Ray Diffraction 3.1043 3.215 -- 134 2636 0.2051 0.2562 -- 99.0
X Ray Diffraction 3.215 3.3434 -- 156 2665 0.2011 0.2616 -- 99.0
X Ray Diffraction 3.3434 3.4952 -- 142 2695 0.1971 0.2473 -- 99.0
X Ray Diffraction 3.4952 3.6789 -- 126 2697 0.1867 0.233 -- 99.0
X Ray Diffraction 3.6789 3.9086 -- 148 2697 0.1769 0.2074 -- 99.0
X Ray Diffraction 3.9086 4.2091 -- 143 2714 0.1593 0.199 -- 99.0
X Ray Diffraction 4.2091 4.6302 -- 148 2739 0.1511 0.1833 -- 100.0
X Ray Diffraction 4.6302 5.2947 -- 164 2746 0.1433 0.1736 -- 100.0
X Ray Diffraction 5.2947 6.6498 -- 157 2785 0.1739 0.2042 -- 100.0
X Ray Diffraction 6.6498 24.974 -- 146 2855 0.1905 0.1992 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.282
Anisotropic B[1][1] 5.921
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.876
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.797
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.819
f_plane_restr 0.006
f_chiral_restr 0.064
f_angle_d 1.051
f_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.286
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10791
Nucleic Acid Atoms 0
Heterogen Atoms 296
Solvent Atoms 1521

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
SAINT Data Reduction (intensity integration)
SADABS Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine) refinement
Phaser model building
PROTEUM version: PLUS data collection