X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 282.0
Details 1.9-2.1M Ammonium Sulfate, 100mM Na Acetate pH 4.2-4.6, VAPOR DIFFUSION, SITTING DROP, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.13 α = 90
b = 78.13 β = 90
c = 230.91 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 9 -- 2001-11-16
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.976 SSRL BL11-1

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
1.72 43.92 94.8 0.072 -- -- 2.4 -- 40379 -- -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)
1.72 1.78 99.0 0.418 -- 1.65 1.9 16675

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 1.72 43.85 -- 0.0 45030 40379 4458 -- 0.226 0.226 0.223 0.24 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 1.72 1.765 2855 337 2855 0.304 0.311 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.691
Anisotropic B[1][1] 0.59
Anisotropic B[1][2] 0.29
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.88
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.352
r_scbond_it 1.902
r_bond_refined_d 0.011
r_angle_refined_deg 1.142
r_dihedral_angle_1_deg 3.641
r_dihedral_angle_3_deg 13.217
r_chiral_restr 0.077
r_gen_planes_refined 0.004
r_nbd_refined 0.219
r_xyhbond_nbd_refined 0.11
r_symmetry_hbond_refined 0.499
r_symmetry_vdw_refined 0.154
r_mcbond_it 0.57
r_mcangle_it 1.135
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1531
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 148

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
HKL-2000 data collection