X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 4.5
Temperature 291.0
Details 20% PEG 3350, 0.2M Lithium citrate, pH 4.5, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.53 α = 90
b = 118.28 β = 90
c = 156.84 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
IMAGE PLATE RIGAKU RAXIS -- 2007-04-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E DW 1.5418 -- --

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
2.1 20 99.8 0.151 -- -- 6.5 -- 69383 -- -- --
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)
2.1 2.17 99.4 0.945 -- -- 6.2 6812

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 2.27 20.0 -- 0.0 -- 55104 2589 99.583 -- 0.215 0.213 0.267 Thin resolution 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 2.27 2.328 -- 0 3902 0.275 -- -- 98.66
X Ray Diffraction 2.328 2.391 -- 421 3450 0.227 0.329 -- 99.691
X Ray Diffraction 2.391 2.459 -- 0 3810 0.238 -- -- 99.764
X Ray Diffraction 2.459 2.534 -- 380 3312 0.217 0.275 -- 99.865
X Ray Diffraction 2.534 2.616 -- 0 3545 0.22 -- -- 99.747
X Ray Diffraction 2.616 2.706 -- 321 3132 0.221 0.275 -- 99.913
X Ray Diffraction 2.706 2.806 -- 0 3367 0.23 -- -- 99.704
X Ray Diffraction 2.806 2.918 -- 265 2970 0.213 0.293 -- 99.815
X Ray Diffraction 2.918 3.045 -- 240 2865 0.209 0.278 -- 99.807
X Ray Diffraction 3.045 3.19 -- 0 2978 0.217 -- -- 99.899
X Ray Diffraction 3.19 3.358 -- 208 2619 0.213 0.293 -- 99.612
X Ray Diffraction 3.358 3.555 -- 0 2676 0.213 -- -- 99.038
X Ray Diffraction 3.555 3.792 -- 158 2353 0.217 0.321 -- 98.897
X Ray Diffraction 3.792 4.084 -- 138 2244 0.187 0.201 -- 99.25
X Ray Diffraction 4.084 4.455 -- 139 2065 0.165 0.197 -- 99.729
X Ray Diffraction 4.455 4.95 -- 96 1936 0.173 0.188 -- 99.902
X Ray Diffraction 4.95 5.658 -- 66 1734 0.204 0.305 -- 99.723
X Ray Diffraction 5.658 6.795 -- 62 1512 0.244 0.339 -- 99.747
X Ray Diffraction 6.795 9.099 -- 40 1243 0.22 0.281 -- 99.922
X Ray Diffraction 9.099 20.0 -- 55 802 0.263 0.243 -- 98.393
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.166
Anisotropic B[1][1] -0.928
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.459
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.531
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.064
r_angle_refined_deg 1.423
r_dihedral_angle_2_deg 39.228
r_dihedral_angle_3_deg 15.173
r_dihedral_angle_1_deg 5.373
r_bond_refined_d 0.015
r_scangle_it 3.392
r_mcbond_it 1.993
r_mcbond_other 0.483
r_mcangle_it 3.197
r_scbond_it 2.219
r_bond_other_d 0.002
r_gen_planes_other 0.002
r_angle_other_deg 1.823
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 17.393
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7566
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 142

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.4.0069
PDB_EXTRACT data extraction version: 3.005