X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.7
Temperature 280.0
Details ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.66 α = 90
b = 154.52 β = 90
c = 165.64 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2005-03-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, Hamburg BW7B

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 19.62 83.0 0.089 -- -- 4.6 165388 165340 2.0 3.7 12.9
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 1.62 0.759 0.343 -- 2.4 3.1 --

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 1.6 19.62 -- 2.0 165388 165339 3328 82.942 0.159 0.159 0.1583 0.1804 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 1.599 1.64 -- 237 10777 0.187 0.234 -- 75.542
X Ray Diffraction 1.64 1.685 -- 228 10979 0.186 0.211 -- 78.31
X Ray Diffraction 1.685 1.734 -- 235 12164 0.182 0.216 -- 89.452
X Ray Diffraction 1.734 1.788 -- 214 11637 0.172 0.2 -- 88.0
X Ray Diffraction 1.788 1.846 -- 220 10707 0.17 0.19 -- 83.361
X Ray Diffraction 1.846 1.911 -- 212 10664 0.161 0.175 -- 85.881
X Ray Diffraction 1.911 1.983 -- 213 10541 0.151 0.181 -- 87.788
X Ray Diffraction 1.983 2.064 -- 208 9737 0.156 0.168 -- 84.487
X Ray Diffraction 2.064 2.156 -- 189 9509 0.154 0.177 -- 85.815
X Ray Diffraction 2.156 2.261 -- 172 8949 0.155 0.188 -- 84.383
X Ray Diffraction 2.261 2.383 -- 180 8359 0.153 0.178 -- 82.967
X Ray Diffraction 2.383 2.528 -- 150 7964 0.157 0.176 -- 83.263
X Ray Diffraction 2.528 2.702 -- 165 7445 0.16 0.191 -- 82.871
X Ray Diffraction 2.702 2.918 -- 121 6891 0.162 0.195 -- 82.137
X Ray Diffraction 2.918 3.196 -- 156 6236 0.158 0.181 -- 80.83
X Ray Diffraction 3.196 3.573 -- 131 5572 0.147 0.164 -- 79.773
X Ray Diffraction 3.573 4.125 -- 102 4902 0.135 0.153 -- 78.927
X Ray Diffraction 4.125 5.05 -- 79 4139 0.136 0.133 -- 78.155
X Ray Diffraction 5.05 7.131 -- 74 3175 0.186 0.178 -- 76.682
X Ray Diffraction 7.131 94.072 -- 42 1664 0.164 0.211 -- 70.119
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.157
Anisotropic B[1][1] 1.141
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.663
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.477
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 17.946
r_bond_refined_d 0.009
r_scangle_it 2.891
r_xyhbond_nbd_refined 0.095
r_metal_ion_refined 0.025
r_scbond_it 1.736
r_symmetry_hbond_refined 0.102
r_dihedral_angle_3_deg 12.261
r_chiral_restr 0.082
r_mcangle_it 0.918
r_dihedral_angle_1_deg 5.867
r_symmetry_vdw_refined 0.192
r_nbtor_refined 0.303
r_mcbond_it 0.47
r_angle_refined_deg 1.318
r_nbd_refined 0.198
r_gen_planes_refined 0.005
r_dihedral_angle_2_deg 38.842
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9046
Nucleic Acid Atoms 0
Heterogen Atoms 178
Solvent Atoms 1030

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: refmac_5.2.0005
PDB_EXTRACT data extraction version: 1.700
MOLREP phasing