X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details PEG MME 5000, ZnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 277.91 α = 90
b = 38.24 β = 108.99
c = 95.91 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-05-13
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-002+ 1.5418 -- --

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
2.2 19.86 98.5 0.07 -- -- 7.96 -- 48616 -- -- --
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)
2.2 2.28 99.7 0.328 -- 4.8 8.16 --

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 2.2 19.86 -- 1.34 -- 48352 2433 97.95 -- 0.2293 0.227 0.2712 --
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 2.2 2.2449 -- 156 2737 0.2607 0.3418 -- 99.0
X Ray Diffraction 2.2449 2.2936 -- 119 2674 0.2467 0.3223 -- 100.0
X Ray Diffraction 2.2936 2.3469 -- 135 2745 0.2525 0.324 -- 99.0
X Ray Diffraction 2.3469 2.4055 -- 158 2722 0.2447 0.3005 -- 99.0
X Ray Diffraction 2.4055 2.4704 -- 152 2643 0.2436 0.3197 -- 99.0
X Ray Diffraction 2.4704 2.5429 -- 136 2779 0.2628 0.3546 -- 99.0
X Ray Diffraction 2.5429 2.6248 -- 136 2661 0.2592 0.3325 -- 99.0
X Ray Diffraction 2.6248 2.7184 -- 160 2739 0.2591 0.3231 -- 99.0
X Ray Diffraction 2.7184 2.827 -- 127 2647 0.2597 0.3118 -- 98.0
X Ray Diffraction 2.827 2.9552 -- 143 2716 0.2436 0.2882 -- 98.0
X Ray Diffraction 2.9552 3.1105 -- 145 2662 0.238 0.2507 -- 97.0
X Ray Diffraction 3.1105 3.3045 -- 129 2656 0.2164 0.2766 -- 96.0
X Ray Diffraction 3.3045 3.5584 -- 137 2620 0.2068 0.2731 -- 95.0
X Ray Diffraction 3.5584 3.914 -- 152 2613 0.1937 0.2292 -- 95.0
X Ray Diffraction 3.914 4.4747 -- 132 2638 0.1742 0.213 -- 95.0
X Ray Diffraction 4.4747 5.6164 -- 147 2778 0.1812 0.2003 -- 98.0
X Ray Diffraction 5.6164 19.8644 -- 169 2889 0.2527 0.2759 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.633
Anisotropic B[1][1] -1.844
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.415
Anisotropic B[2][2] 7.569
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.725
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.187
f_chiral_restr 0.089
f_bond_d 0.006
f_plane_restr 0.005
f_dihedral_angle_d 19.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6651
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 521

Software

Software
Software Name Purpose
d*TREK data processing version: 9.4SSI
PHENIX refinement version: 1.4_4
PDB_EXTRACT data extraction version: 3.005
CrystalClear data collection
d*TREK data reduction
d*TREK data scaling
PHASER phasing