X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 298.0
Details 13 % PEG 3350, 0.2M CaCl2, 0.1M MES, 1% ethanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.93 α = 90
b = 67.61 β = 90.12
c = 167 γ = 90
Symmetry
Space Group P 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Bruker Platinum 135 Montel multilayer 2008-05-23
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
2.4 30 90.1 -- 0.088 -- 4.7 59401 53699 -- -- 34.6
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)
2.4 2.5 72.5 -- 0.281 4.9 2.7 4944

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 2.4 29.948 -- 0.06 -- 53699 2051 90.09 -- 0.24 0.237 0.309 random with consideration of twin law h, -k, -l
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 2.4 2.4414 -- 75 1904 0.2981 0.4209 -- 98.0
X Ray Diffraction 2.4414 2.4857 -- 85 2104 0.2874 0.2904 -- 98.0
X Ray Diffraction 2.4857 2.5335 -- 93 2298 0.2801 0.318 -- 98.0
X Ray Diffraction 2.5335 2.5852 -- 94 2525 0.2736 0.3765 -- 98.0
X Ray Diffraction 2.5852 2.6414 -- 110 2702 0.2865 0.3522 -- 98.0
X Ray Diffraction 2.6414 2.7028 -- 102 2770 0.2782 0.3387 -- 98.0
X Ray Diffraction 2.7028 2.7703 -- 104 2728 0.2768 0.3799 -- 98.0
X Ray Diffraction 2.7703 2.8452 -- 105 2744 0.2707 0.3601 -- 98.0
X Ray Diffraction 2.8452 2.9288 -- 111 2717 0.2703 0.3214 -- 98.0
X Ray Diffraction 2.9288 3.0233 -- 101 2676 0.2646 0.2992 -- 98.0
X Ray Diffraction 3.0233 3.1312 -- 103 2680 0.2428 0.3367 -- 98.0
X Ray Diffraction 3.1312 3.2565 -- 106 2689 0.2464 0.3323 -- 98.0
X Ray Diffraction 3.2565 3.4045 -- 98 2668 0.2278 0.3467 -- 98.0
X Ray Diffraction 3.4045 3.5837 -- 105 2681 0.2201 0.3024 -- 98.0
X Ray Diffraction 3.5837 3.8078 -- 99 2643 0.2093 0.2687 -- 98.0
X Ray Diffraction 3.8078 4.1011 -- 107 2667 0.1912 0.242 -- 98.0
X Ray Diffraction 4.1011 4.5126 -- 98 2662 0.1783 0.2684 -- 98.0
X Ray Diffraction 4.5126 5.1627 -- 107 2638 0.1955 0.2225 -- 98.0
X Ray Diffraction 5.1627 6.4935 -- 108 2652 0.2512 0.3793 -- 98.0
X Ray Diffraction 6.4935 29.9503 -- 95 2545 0.256 0.3088 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.136
Anisotropic B[1][1] -4.628
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.09
Anisotropic B[2][2] -4.972
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.389
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.971
f_plane_restr 0.004
f_chiral_restr 0.053
f_angle_d 0.836
f_bond_d 0.004
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.495
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10663
Nucleic Acid Atoms 0
Heterogen Atoms 176
Solvent Atoms 371

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
pdb_extract version: 3.006 data extraction
phenix refinement