X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.1-M HEPES, 10% ISOPROPANOL, 19% PEG 4000, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.05 α = 90
b = 63.99 β = 91.53
c = 39.45 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate OSMIC MIRRORS 2001-03-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

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
1.9 99 96.7 -- 0.06 -- 2.2 14294 14294 -- -3.0 --
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)
1.9 1.97 96.1 -- 0.22 6.0 1.9 1411

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
FOURIER SYNTHESIS 1.9 48.8 -- -- 14330 13599 731 96.9 -- 0.18808 0.18495 0.24753 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 1.9 2.0 1986 113 -- 0.33 0.42 -- 98.04
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.566
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.14
Anisotropic B[2][2] -1.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.64
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.209
r_gen_planes_refined 0.008
r_chiral_restr 0.152
r_dihedral_angle_2_deg 16.879
r_dihedral_angle_1_deg 5.123
r_angle_refined_deg 1.541
r_bond_refined_d 0.017
r_xyhbond_nbd_refined 0.179
r_symmetry_vdw_refined 0.314
r_symmetry_hbond_refined 0.135
r_mcbond_it 4.556
r_mcangle_it 6.837
r_scbond_it 5.709
r_scangle_it 8.136
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1245
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 58

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection