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 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 2.2 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.6 α = 90
b = 99.2 β = 90
c = 66.6 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 169
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2001-07-21
Diffraction Radiation
Monochromator Protocol
OSMIC MIRRORS 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
2.5 33.3 94.8 0.108 -- -- 3.1 -- 21432 -- 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)
2.5 2.7 89.7 0.294 -- 2.4 2.8 4098

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 2.5 10.0 -- -- -- 17847 2021 88.8 -- 0.19232 0.18435 0.26377 MATCHED TO PDB ENTRY 1Y22
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 2.5 2.686 -- 336 2946 0.25 0.363 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.841
Anisotropic B[1][1] 1.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.59
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_other 0.114
r_dihedral_angle_3_deg 21.432
r_scbond_it 2.198
r_nbd_refined 0.271
r_nbd_other 0.226
r_angle_other_deg 1.232
r_mcbond_it 0.87
r_symmetry_hbond_refined 0.597
r_chiral_restr 0.102
r_dihedral_angle_1_deg 4.008
r_scangle_it 3.604
r_xyhbond_nbd_refined 0.248
r_gen_planes_refined 0.006
r_bond_refined_d 0.024
r_bond_other_d 0.001
r_gen_planes_other 0.005
r_symmetry_vdw_refined 0.455
r_mcangle_it 1.627
r_symmetry_vdw_other 0.197
r_angle_refined_deg 1.881
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4382
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 135

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
X-PLOR model building
REFMAC refinement version: 5.0
CCP4 data scaling version: (SCALA)
X-PLOR phasing