X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 291.0
Details 18% PEG3350, 0.2M ammonium dihydrogen phosphate, 0.1M HEPES, pH 7.0, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.66 α = 90
b = 109.21 β = 90
c = 157.95 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2006-07-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.97625 APS 22-ID

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
1.6 50 77.3 0.065 -- -- 6.4 -- 93258 -- -- --
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)
1.6 1.66 -- 0.544 -- -- 1.3 --

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 1.8 30.0 -- -- -- 83039 2110 97.353 0.193 -- 0.1924 0.2267 thin shells
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 1.8 1.847 -- 10 4988 0.265 0.352 -- 80.173
X Ray Diffraction 1.847 1.897 -- 0 5458 0.243 -- -- 90.215
X Ray Diffraction 1.897 1.952 -- 0 5795 0.223 -- -- 97.789
X Ray Diffraction 1.952 2.012 -- 528 5088 0.211 0.278 -- 98.995
X Ray Diffraction 2.012 2.077 -- 0 5513 0.204 -- -- 99.048
X Ray Diffraction 2.077 2.15 -- 0 5315 0.192 -- -- 99.364
X Ray Diffraction 2.15 2.23 -- 446 4750 0.19 0.233 -- 99.331
X Ray Diffraction 2.23 2.321 -- 0 4983 0.184 -- -- 99.421
X Ray Diffraction 2.321 2.424 -- 0 4783 0.189 -- -- 99.584
X Ray Diffraction 2.424 2.541 -- 361 4234 0.193 0.231 -- 99.653
X Ray Diffraction 2.541 2.677 -- 0 4380 0.19 -- -- 99.613
X Ray Diffraction 2.677 2.838 -- 253 3898 0.195 0.225 -- 99.736
X Ray Diffraction 2.838 3.032 -- 0 3946 0.2 -- -- 99.848
X Ray Diffraction 3.032 3.273 -- 202 3475 0.198 0.22 -- 99.918
X Ray Diffraction 3.273 3.581 -- 0 3372 0.187 -- -- 99.911
X Ray Diffraction 3.581 3.996 -- 128 2970 0.171 0.198 -- 99.968
X Ray Diffraction 3.996 4.601 -- 0 2747 0.155 -- -- 100.0
X Ray Diffraction 4.601 5.602 -- 88 2282 0.174 0.183 -- 99.958
X Ray Diffraction 5.602 7.788 -- 57 1826 0.234 0.289 -- 99.947
X Ray Diffraction 7.788 30.0 -- 37 1126 0.214 0.24 -- 98.979
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.93
Anisotropic B[1][1] 1.114
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.183
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.931
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 36.4
r_chiral_restr 0.094
r_mcbond_other 0.808
r_bond_other_d 0.001
r_nbtor_refined 0.185
r_metal_ion_refined 0.192
r_dihedral_angle_4_deg 14.777
r_gen_planes_other 0.001
r_angle_refined_deg 1.459
r_symmetry_vdw_refined 0.127
r_scangle_it 4.096
r_symmetry_hbond_refined 0.054
r_nbd_refined 0.217
r_dihedral_angle_1_deg 5.568
r_xyhbond_nbd_refined 0.142
r_bond_refined_d 0.018
r_mcbond_it 3.041
r_symmetry_vdw_other 0.202
r_nbd_other 0.199
r_angle_other_deg 0.955
r_gen_planes_refined 0.007
r_scbond_it 3.054
r_mcangle_it 3.79
r_dihedral_angle_3_deg 13.338
r_nbtor_other 0.086
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5619
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 252

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: refmac_5.2.0019
PDB_EXTRACT data extraction version: 1.701
ARP/wARP model building
MolProbity model building
Coot model building