X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.8
Temperature 298.0
Details PEG 3000, sodium chloride, spermine, HEPES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.8 α = 90
b = 104.72 β = 90
c = 193.92 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 CUSTOM-MADE -- 2002-08-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 1.0332 APS 19-BM

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
2.3 95.65 93.65 -- 0.085 -- 4.7 43799 41018 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)
2.3 2.36 61.9 -- 0.339 2.08 -- --

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 2.3 95.35 -- 0.0 43799 41018 2169 93.65 0.2083 0.2083 0.20601 0.25185 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 2.3 2.36 -- 106 2019 0.268 0.318 -- 61.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.253
Anisotropic B[1][1] -2.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.8
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.014
r_dihedral_angle_1_deg 6.748
r_scangle_it 1.819
r_xyhbond_nbd_refined 0.345
r_chiral_restr 0.096
r_symmetry_hbond_refined 0.092
r_mcangle_it 2.089
r_scbond_it 1.177
r_mcbond_it 1.205
r_symmetry_vdw_refined 0.218
r_angle_refined_deg 1.387
r_gen_planes_refined 0.006
r_nbd_refined 0.204
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6888
Nucleic Acid Atoms 82
Heterogen Atoms 6
Solvent Atoms 96

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
HKL-2000 data reduction
SCALEPACK data scaling
AMoRE phasing