X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.93 α = 90
b = 136.66 β = 90
c = 45.23 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-05-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0000 ESRF ID23-1

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 73.95 99.9 -- 0.106 6.584 3.8 37692 37692 -- -- 34.17
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)
2.0 2.11 100.0 0.623 0.623 1.2 3.9 5408

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 2.0 42.98 -- 0.0 -- 37651 1885 99.82 -- 0.2026 0.2009 0.2345 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 2.0 2.052 -- 129 2613 0.267 0.283 -- 100.0
X Ray Diffraction 2.052 2.108 -- 117 2542 0.253 0.29 -- 100.0
X Ray Diffraction 2.108 2.169 -- 154 2450 0.248 0.281 -- 100.0
X Ray Diffraction 2.169 2.236 -- 129 2389 0.227 0.243 -- 100.0
X Ray Diffraction 2.236 2.309 -- 123 2336 0.22 0.292 -- 100.0
X Ray Diffraction 2.309 2.39 -- 120 2285 0.232 0.285 -- 100.0
X Ray Diffraction 2.39 2.48 -- 110 2176 0.216 0.23 -- 99.956
X Ray Diffraction 2.48 2.581 -- 115 2096 0.22 0.262 -- 99.955
X Ray Diffraction 2.581 2.696 -- 109 2013 0.207 0.215 -- 100.0
X Ray Diffraction 2.696 2.827 -- 108 1966 0.21 0.246 -- 100.0
X Ray Diffraction 2.827 2.98 -- 102 1807 0.21 0.258 -- 99.948
X Ray Diffraction 2.98 3.161 -- 93 1753 0.194 0.198 -- 99.784
X Ray Diffraction 3.161 3.378 -- 95 1654 0.198 0.204 -- 99.829
X Ray Diffraction 3.378 3.648 -- 101 1514 0.189 0.224 -- 99.938
X Ray Diffraction 3.648 3.996 -- 66 1444 0.175 0.232 -- 99.802
X Ray Diffraction 3.996 4.466 -- 60 1303 0.152 0.196 -- 99.489
X Ray Diffraction 4.466 5.153 -- 34 1195 0.153 0.193 -- 99.838
X Ray Diffraction 5.153 6.304 -- 45 998 0.19 0.246 -- 99.239
X Ray Diffraction 6.304 8.883 -- 57 768 0.195 0.201 -- 98.802
X Ray Diffraction 8.883 73.948 -- 18 464 0.226 0.227 -- 94.882
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.105
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.15
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.881
r_dihedral_angle_4_deg 13.622
r_mcbond_other 1.522
r_dihedral_angle_2_deg 32.578
r_angle_other_deg 0.681
r_mcangle_it 2.443
r_bond_refined_d 0.005
r_dihedral_angle_3_deg 12.34
r_gen_planes_other 0.001
r_angle_refined_deg 1.053
r_gen_planes_refined 0.004
r_mcbond_it 1.522
r_chiral_restr 0.068
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 52
Solvent Atoms 104

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
XDS data scaling
REFMAC refinement version: refmac_5.7.0032
Coot model building
PDB_EXTRACT data extraction version: 3.14