X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 6.5
Temperature 288.0
Details Equal volumes of precipitant, protein solution and DNA. Precipitant: Optimized index screen 79- 25 mM bis-tris, 25% PEG 3000, 50 mM ammonium acetate. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.96 α = 90
b = 300.3 β = 90
c = 46 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2009-04-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-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
2.9 50 92.7 0.065 -- -- 3.7 -- 17712 -- -- 99.4
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)
2.9 2.95 92.9 0.503 -- -- 3.3 875

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 3.0 31.66 -- 0.0 -- 15998 820 92.52 -- 0.1877 0.1845 0.2452 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 3.0 3.078 -- 61 1039 0.272 0.374 -- 96.32
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.0928
Anisotropic B[1][1] 8.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.0
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.069
r_dihedral_angle_4_deg 16.114
r_dihedral_angle_3_deg 17.601
r_dihedral_angle_2_deg 33.475
r_dihedral_angle_1_deg 5.289
r_angle_other_deg 0.842
r_angle_refined_deg 1.143
r_bond_other_d 0.001
r_bond_refined_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2872
Nucleic Acid Atoms 2038
Heterogen Atoms 0
Solvent Atoms 3

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Molecular Replacement Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
SCALEPACK data reduction
DENZO data collection