X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 10% PEG3350, 0.1M ammonium formate, 0.2M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.36 α = 90
b = 108.71 β = 90
c = 54.94 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Bruker DIP-6040 -- 2007-12-02
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU

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
1.52 50 100.0 0.06 0.06 -- 5.7 -- 43495 0.0 -3.0 14.3
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)
1.52 1.55 100.0 0.492 0.492 4.16 5.7 --

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 1.52 33.78 0.0 0.0 3137 43450 2187 99.83 -- 0.1789 0.1773 0.21 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 1.518 1.558 3137 167 2970 0.204 0.238 -- 98.339
X Ray Diffraction 1.558 1.6 3074 163 2911 0.191 0.223 -- 100.0
X Ray Diffraction 1.6 1.646 3009 153 2856 0.184 0.24 -- 99.967
X Ray Diffraction 1.646 1.697 2922 153 2769 0.192 0.265 -- 99.932
X Ray Diffraction 1.697 1.753 2848 147 2701 0.183 0.227 -- 99.965
X Ray Diffraction 1.753 1.814 2733 140 2593 0.171 0.196 -- 99.927
X Ray Diffraction 1.814 1.882 2670 131 2539 0.173 0.209 -- 99.963
X Ray Diffraction 1.882 1.959 2572 125 2447 0.172 0.187 -- 100.0
X Ray Diffraction 1.959 2.046 2470 130 2340 0.172 0.198 -- 99.96
X Ray Diffraction 2.046 2.145 2330 106 2224 0.173 0.213 -- 100.0
X Ray Diffraction 2.145 2.26 2246 101 2145 0.166 0.171 -- 100.0
X Ray Diffraction 2.26 2.397 2244 112 2019 0.166 0.219 -- 99.953
X Ray Diffraction 2.397 2.562 2002 87 1915 0.168 0.205 -- 100.0
X Ray Diffraction 2.562 2.765 1874 105 1769 0.192 0.241 -- 100.0
X Ray Diffraction 2.765 3.027 1729 86 1643 0.179 0.223 -- 99.942
X Ray Diffraction 3.027 3.381 1574 71 1503 0.171 0.196 -- 99.937
X Ray Diffraction 3.381 3.898 1405 76 1329 0.166 0.18 -- 99.929
X Ray Diffraction 3.898 4.758 1198 58 1140 0.159 0.217 -- 99.917
X Ray Diffraction 4.758 6.663 945 57 888 0.206 0.198 -- 99.894
X Ray Diffraction 6.663 33.781 581 19 562 0.218 0.222 -- 99.147
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.8864
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.228
r_scbond_it 3.293
r_angle_refined_deg 1.743
r_dihedral_angle_2_deg 36.072
r_dihedral_angle_4_deg 17.139
r_scangle_it 5.127
r_dihedral_angle_1_deg 5.163
r_chiral_restr 0.109
r_gen_planes_refined 0.01
r_mcbond_it 1.245
r_bond_refined_d 0.019
r_dihedral_angle_3_deg 14.029
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2348
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 291

Software

Software
Software Name Purpose
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement version: refmac_5.5.0109
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data reduction