X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.89 α = 90
b = 39.46 β = 99.92
c = 54.13 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 300 mm CCD -- 2012-01-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

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
2.05 34.42 99.79 0.053 -- -- 3.71 -- 9281 -- -- --
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)
2.05 2.16 99.85 0.67 -- -- 3.71 1345

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 2.05 30.0 -- 0.0 -- 9281 452 99.678 -- 0.217 0.2155 0.2434 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 2.05 2.103 -- 32 651 0.321 0.415 -- 99.708
X Ray Diffraction 2.103 2.16 -- 30 631 0.278 0.345 -- 100.0
X Ray Diffraction 2.16 2.223 -- 35 628 0.268 0.288 -- 100.0
X Ray Diffraction 2.223 2.291 -- 27 568 0.267 0.297 -- 99.832
X Ray Diffraction 2.291 2.365 -- 24 601 0.243 0.187 -- 99.84
X Ray Diffraction 2.365 2.448 -- 32 542 0.232 0.292 -- 99.653
X Ray Diffraction 2.448 2.54 -- 25 531 0.238 0.312 -- 99.642
X Ray Diffraction 2.54 2.642 -- 28 527 0.257 0.365 -- 100.0
X Ray Diffraction 2.642 2.759 -- 19 490 0.288 0.264 -- 99.414
X Ray Diffraction 2.759 2.892 -- 22 499 0.287 0.278 -- 100.0
X Ray Diffraction 2.892 3.047 -- 33 436 0.24 0.312 -- 100.0
X Ray Diffraction 3.047 3.23 -- 28 424 0.25 0.289 -- 99.779
X Ray Diffraction 3.23 3.45 -- 25 399 0.178 0.244 -- 99.531
X Ray Diffraction 3.45 3.723 -- 14 382 0.2 0.178 -- 99.748
X Ray Diffraction 3.723 4.072 -- 24 353 0.189 0.201 -- 99.472
X Ray Diffraction 4.072 4.542 -- 17 317 0.166 0.135 -- 99.701
X Ray Diffraction 4.542 5.224 -- 14 282 0.191 0.225 -- 99.663
X Ray Diffraction 5.224 6.351 -- 8 249 0.183 0.223 -- 100.0
X Ray Diffraction 6.351 8.786 -- 7 196 0.188 0.192 -- 99.024
X Ray Diffraction 8.786 30.0 -- 8 120 0.193 0.266 -- 98.462
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.769
Anisotropic B[1][1] -1.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.395
Anisotropic B[2][2] -0.739
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.875
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.064
r_dihedral_angle_4_deg 20.48
r_dihedral_angle_3_deg 14.94
r_dihedral_angle_2_deg 40.342
r_dihedral_angle_1_deg 6.013
r_angle_other_deg 1.16
r_angle_refined_deg 1.359
r_bond_other_d 0.003
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 384
Nucleic Acid Atoms 486
Heterogen Atoms 5
Solvent Atoms 23

Software

Computing
Computing Package Purpose
xds Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.7.0027 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.7.0027 refinement
Phaser molecular replacement
SCALA version: CCP4_3.3.20 data reduction