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_angle_d 0.836
f_bond_d 0.004
f_chiral_restr 0.053
f_plane_restr 0.004
f_dihedral_angle_d 16.971
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

Software
Software Name Purpose
PHENIX refinement
PDB_EXTRACT data extraction version: 3.006
PROTEUM PLUS data collection version: PLUS
SAINT data reduction
SADABS data scaling
PHASER phasing