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, 5% MPD, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.03 α = 90
b = 39.52 β = 91.03
c = 57.63 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 -- 2012-01-26
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
2.25 35.51 99.9 0.046 -- -- 4.12 -- 7738 -- -- --
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)
2.25 2.37 100.0 0.49 -- -- 4.17 1110

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 2.25 35.0 -- 0.0 -- 7736 351 99.781 -- 0.221 0.2196 0.2502 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 2.25 2.308 -- 26 539 0.467 0.466 -- 100.0
X Ray Diffraction 2.308 2.371 -- 23 515 0.442 0.575 -- 100.0
X Ray Diffraction 2.371 2.44 -- 24 512 0.38 0.528 -- 99.814
X Ray Diffraction 2.44 2.514 -- 23 498 0.364 0.405 -- 99.808
X Ray Diffraction 2.514 2.596 -- 19 488 0.339 0.459 -- 100.0
X Ray Diffraction 2.596 2.687 -- 28 458 0.324 0.371 -- 100.0
X Ray Diffraction 2.687 2.788 -- 18 455 0.315 0.327 -- 100.0
X Ray Diffraction 2.788 2.901 -- 23 445 0.292 0.359 -- 99.787
X Ray Diffraction 2.901 3.029 -- 23 404 0.262 0.347 -- 100.0
X Ray Diffraction 3.029 3.175 -- 21 395 0.257 0.258 -- 99.76
X Ray Diffraction 3.175 3.346 -- 12 393 0.198 0.217 -- 99.754
X Ray Diffraction 3.346 3.547 -- 15 350 0.198 0.252 -- 99.455
X Ray Diffraction 3.547 3.789 -- 10 346 0.214 0.173 -- 99.72
X Ray Diffraction 3.789 4.088 -- 20 321 0.183 0.249 -- 100.0
X Ray Diffraction 4.088 4.472 -- 17 293 0.157 0.211 -- 100.0
X Ray Diffraction 4.472 4.99 -- 12 273 0.167 0.176 -- 100.0
X Ray Diffraction 4.99 5.743 -- 11 237 0.172 0.167 -- 99.598
X Ray Diffraction 5.743 6.986 -- 10 202 0.192 0.221 -- 100.0
X Ray Diffraction 6.986 9.689 -- 10 160 0.172 0.279 -- 99.415
X Ray Diffraction 9.689 35.0 -- 6 100 0.178 0.161 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 70.547
Anisotropic B[1][1] -2.092
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.375
Anisotropic B[2][2] -3.406
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.448
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.061
r_dihedral_angle_4_deg 17.228
r_dihedral_angle_3_deg 15.397
r_dihedral_angle_2_deg 33.295
r_dihedral_angle_1_deg 5.478
r_angle_other_deg 1.155
r_angle_refined_deg 1.377
r_bond_other_d 0.003
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 383
Nucleic Acid Atoms 487
Heterogen Atoms 2
Solvent Atoms 10

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