X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details 20 MG/ML PROTEIN, 16% PEG 5K MME, 100 MM IMIDAZOLE, PH 7.5, 5% ISOPROPANOL

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.81 α = 90
b = 45.88 β = 90
c = 85.74 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC TORROIDAL MIRROR 2002-09-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 -- ESRF ID29

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
1.05 20 98.0 0.062 -- -- 4.7 -- 121638 -- -- --
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)
1.05 1.09 86.4 0.441 -- 2.3 2.05 --

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 1.05 19.8 -- -- -- 112969 5945 97.9 -- 0.104 0.103 0.126 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 1.05 1.08 -- 360 7089 0.258 0.286 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.12
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.15
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.558
r_scbond_it 3.441
r_mcangle_it 2.81
r_mcbond_it 2.03
r_nbd_refined 0.318
r_gen_planes_other 0.0
r_gen_planes_refined 0.004
r_chiral_restr 0.126
r_dihedral_angle_1_deg 6.229
r_angle_other_deg 0.85
r_angle_refined_deg 1.689
r_bond_other_d 0.0
r_bond_refined_d 0.015
r_nbd_other 0.455
r_nbtor_other 0.298
r_metal_ion_refined 0.614
r_metal_ion_other 0.335
r_symmetry_vdw_refined 0.382
r_symmetry_vdw_other 0.427
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2324
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 629

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.1.03 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.03 refinement