X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details NA CACODALYTE, MG ACETATE, PEG 8000 , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.1 α = 90
b = 57.1 β = 90
c = 82.48 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRROR 2002-09-26
Diffraction Radiation
Monochromator Protocol
MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
1.8 30 99.3 -- 0.053 -- 4.0 -- 14856 -- -3.0 28.35
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)
1.8 1.86 95.2 -- 0.854 1.2 3.4 --

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 1.8 28.55 -- 0.0 -- 13300 719 94.0 -- 0.188 0.186 0.227 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 1.8 1.85 -- 41 814 0.356 0.376 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.07
Anisotropic B[1][1] 0.66
Anisotropic B[1][2] 0.33
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.98
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.197
r_symmetry_hbond_refined 0.155
r_symmetry_vdw_refined 0.206
r_scangle_it 4.066
r_nbd_refined 0.219
r_gen_planes_refined 0.008
r_angle_refined_deg 1.666
r_mcangle_it 1.823
r_dihedral_angle_1_deg 5.754
r_bond_refined_d 0.017
r_chiral_restr 0.114
r_mcbond_it 1.017
r_scbond_it 2.552
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 108

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.27 Structure Refinement
Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data reduction
AMORE model building
REFMAC version: 5.1.27 refinement