X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 7.5
Temperature 291.0
Details 0.9M Sodium Acetate, 1mM Triton X-100, 0.1M HEPES, pH 7.5, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.24 α = 90
b = 79.24 β = 94.63
c = 92 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
CCD MARMOSAIC 225 mm CCD Vertical Collimating Mirror, DCM, Toroidal Focusing Mirror 2007-08-01
Diffraction Radiation
Monochromator Protocol
Double Flat Si(111) Crystal Monochromator with Fixed-exit SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45 LNLS W01B-MX2

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
1.9 50 98.8 0.106 -- -- 2.8 -- 27404 -- -- --
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)
1.9 1.97 94.8 0.305 -- -- 2.4 2592

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 1.9 19.811 -- 1.35 27916 27377 1375 98.07 0.1946 0.1946 0.1923 0.2361 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 1.897 1.965 -- 124 2304 0.242 0.317 -- 87.0
X Ray Diffraction 1.965 2.044 -- 145 2614 0.204 0.25 -- 99.0
X Ray Diffraction 2.044 2.136 -- 149 2607 0.172 0.242 -- 99.0
X Ray Diffraction 2.136 2.249 -- 145 2593 0.174 0.235 -- 99.0
X Ray Diffraction 2.249 2.39 -- 141 2601 0.182 0.296 -- 99.0
X Ray Diffraction 2.39 2.574 -- 130 2656 0.192 0.253 -- 99.0
X Ray Diffraction 2.574 2.832 -- 127 2604 0.185 0.233 -- 99.0
X Ray Diffraction 2.832 3.24 -- 129 2662 0.182 0.234 -- 100.0
X Ray Diffraction 3.24 4.077 -- 128 2690 0.171 0.196 -- 100.0
X Ray Diffraction 4.077 19.812 -- 157 2671 0.215 0.23 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 30.241
Anisotropic B[1][1] 0.258
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.449
Anisotropic B[2][2] -0.187
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.071
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.138
f_plane_restr 0.004
f_chiral_restr 0.068
f_angle_d 1.009
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2680
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 309

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL 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
HKL data processing