X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, PH 7.0, BATCH, TEMPERATURE 298K, 1 ATM N2. EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 13% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE. THE CRYSTAL WAS THEN EXPOSED TO AIR AT 298K AND DATA WAS COLLECTED AT 298K.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.3 α = 90
b = 99.1 β = 90
c = 66.8 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SDMS GRAPHITE 1997-12-23
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.73 50 97.9 0.134 -- -- 5.7 -- 17254 0.0 0.0 --
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)
2.73 2.94 90.5 0.301 -- 1.5 4.3 3138

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 2.73 10.0 -- 0.0 -- 15089 1699 97.75 -- 0.19752 0.18993 0.26603 10 SETS MATCHED TO PDB ENTRY 1Y4P
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 2.73 2.931 -- 294 2708 0.249 0.325 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.865
Anisotropic B[1][1] -1.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.47
r_gen_planes_refined 0.003
r_mcangle_it 0.9
r_scangle_it 1.907
r_bond_refined_d 0.019
r_angle_refined_deg 1.378
r_xyhbond_nbd_refined 0.208
r_symmetry_vdw_refined 0.305
r_nbd_refined 0.264
r_scbond_it 1.156
r_dihedral_angle_1_deg 2.483
r_metal_ion_refined 0.031
r_symmetry_hbond_refined 0.163
r_dihedral_angle_3_deg 17.057
r_chiral_restr 0.079
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4376
Nucleic Acid Atoms 0
Heterogen Atoms 176
Solvent Atoms 175

Software

Software
Software Name Purpose
SDMS data collection
SDMS data reduction
X-PLOR model building
REFMAC refinement version: 5.0
SDMS data scaling
X-PLOR phasing