X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 298.0
Details 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.0, batch, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.2 α = 90
b = 98.4 β = 90
c = 66.5 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 2001-09-26
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
2.6 30.43 94.7 0.093 -- -- 3.2 -- 18673 -- 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)
2.6 2.79 89.0 0.208 -- 3.3 3.0 3549

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 2.6 10.0 -- 0.0 -- 15836 1792 90.69 -- 0.18456 0.1749 0.26955 10 SETS MATCHED TO PDB ENTRY 1RQ3
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 2.6 2.793 -- 296 2687 0.199 0.341 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.361
Anisotropic B[1][1] 0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.12
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.242
r_dihedral_angle_3_deg 20.275
r_nbd_refined 0.277
r_symmetry_vdw_refined 0.132
r_mcangle_it 1.721
r_nbd_other 0.226
r_bond_refined_d 0.021
r_scbond_it 2.223
r_angle_refined_deg 1.882
r_dihedral_angle_1_deg 3.817
r_symmetry_hbond_refined 0.287
r_symmetry_vdw_other 0.231
r_mcbond_it 0.928
r_bond_other_d 0.001
r_scangle_it 3.562
r_xyhbond_nbd_other 0.096
r_angle_other_deg 1.17
r_gen_planes_other 0.005
r_gen_planes_refined 0.006
r_chiral_restr 0.095
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4384
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 153

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