X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 28% PEG4000, 8% isopropanol, 0.1M sodium acetate, 10mM L-proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.6 α = 90
b = 113.6 β = 90
c = 50.25 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 Si(111) double-crystal monochromator 2009-08-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-BM 0.97910 APS 17-BM

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
1.95 50 99.6 0.063 -- -- 28.5 -- 12319 -- -- --
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)
1.95 2.02 100.0 0.473 -- -- 29.0 1212

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
SAD 1.95 25.13 -- 0.0 -- 12250 590 99.17 -- 0.216 0.215 0.239 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 1.947 1.997 -- 51 843 0.245 0.317 -- 99.888
X Ray Diffraction 1.997 2.052 -- 47 815 0.247 0.296 -- 99.309
X Ray Diffraction 2.052 2.111 -- 37 808 0.247 0.233 -- 100.0
X Ray Diffraction 2.111 2.175 -- 35 781 0.247 0.242 -- 99.878
X Ray Diffraction 2.175 2.246 -- 36 753 0.22 0.271 -- 99.496
X Ray Diffraction 2.246 2.324 -- 59 706 0.219 0.235 -- 98.837
X Ray Diffraction 2.324 2.411 -- 24 725 0.198 0.275 -- 99.734
X Ray Diffraction 2.411 2.509 -- 30 682 0.228 0.289 -- 98.752
X Ray Diffraction 2.509 2.619 -- 34 664 0.235 0.169 -- 99.572
X Ray Diffraction 2.619 2.745 -- 35 621 0.221 0.292 -- 99.848
X Ray Diffraction 2.745 2.892 -- 33 598 0.239 0.22 -- 98.903
X Ray Diffraction 2.892 3.065 -- 22 575 0.221 0.355 -- 99.5
X Ray Diffraction 3.065 3.273 -- 27 534 0.219 0.171 -- 98.768
X Ray Diffraction 3.273 3.53 -- 25 513 0.211 0.247 -- 99.445
X Ray Diffraction 3.53 3.86 -- 17 476 0.186 0.218 -- 99.596
X Ray Diffraction 3.86 4.303 -- 18 427 0.189 0.194 -- 99.109
X Ray Diffraction 4.303 4.944 -- 24 387 0.174 0.242 -- 100.0
X Ray Diffraction 4.944 5.997 -- 14 337 0.228 0.21 -- 99.716
X Ray Diffraction 5.997 8.25 -- 13 272 0.241 0.24 -- 98.958
X Ray Diffraction 8.25 25.125 -- 9 143 0.228 0.251 -- 80.423
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.967
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.81
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.337
r_angle_refined_deg 1.082
r_chiral_restr 0.082
r_mcangle_it 1.473
r_dihedral_angle_3_deg 13.549
r_gen_planes_refined 0.005
r_bond_refined_d 0.013
r_dihedral_angle_2_deg 38.85
r_dihedral_angle_4_deg 10.084
r_mcbond_it 0.776
r_scbond_it 2.055
r_dihedral_angle_1_deg 4.238
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 931
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 48

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
DM phasing version: 5.0
REFMAC refinement version: refmac_5.5.0102
PDB_EXTRACT data extraction version: 3.005
JDirector data collection
HKL-2000 data reduction
HKL-2000 data scaling