X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 1.4M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.35 α = 90
b = 62.03 β = 102.29
c = 118.13 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors --
Diffraction Radiation
Monochromator Protocol
Si 220 Rosenbaum-Rock double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.9764 APS 22-ID

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
2.4 15 91.4 0.056 0.056 -- 6.3 23288 23288 0.0 0.0 59.22
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)
2.4 2.49 59.1 0.173 0.173 0.076 4.0 1486

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 2.4 10.0 0.0 0.0 22984 22984 2273 90.58 -- 0.212 0.206 0.264 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 2.4 2.459 912 97 815 0.252 0.387 -- 51.12
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 40.708
Anisotropic B[1][1] 0.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.13
Anisotropic B[2][2] 4.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.07
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.217
r_scangle_it 4.999
r_bond_refined_d 0.012
r_angle_refined_deg 1.276
r_dihedral_angle_3_deg 16.812
r_symmetry_vdw_refined 0.246
r_nbtor_refined 0.303
r_dihedral_angle_2_deg 38.91
r_symmetry_hbond_refined 0.176
r_mcbond_it 2.087
r_mcangle_it 2.626
r_chiral_restr 0.078
r_dihedral_angle_4_deg 19.438
r_scbond_it 3.576
r_dihedral_angle_1_deg 5.105
r_gen_planes_refined 0.004
r_xyhbond_nbd_refined 0.216
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4061
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 151

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 2.000
HKL-2000 data collection
HKL-2000 data reduction
MOLREP phasing