X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 290.0
Details PEG8000, Magnesium acetate, Bicine buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61 α = 90
b = 93.6 β = 100.1
c = 85.2 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-09-20
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0597 APS 17-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
2.4 11 99.2 0.045 -- -- 5.3 36364 36364 0.0 0.0 55.0
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)
2.4 2.45 98.9 0.26 -- -- 5.3 --

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
MIR 2.4 10.0 -- 0.0 -- 34399 1836 99.4 -- 0.208 0.204 0.247 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 2.4 2.48 -- 168 3221 0.222 0.264 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.75
Anisotropic B[1][1] -2.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] 1.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.87
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.301
r_gen_planes_refined 0.006
r_chiral_restr 0.099
r_dihedral_angle_1_deg 10.64
r_angle_refined_deg 1.553
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.201
r_symmetry_vdw_refined 0.346
r_symmetry_hbond_refined 0.261
r_mcbond_it 7.259
r_mcangle_it 9.664
r_scbond_it 12.208
r_scangle_it 12.65
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5243
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 484

Software

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