X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 294.0
Details PEG 4000, Tris-HCl, Lithium sulfate, methylpentane diol, pH 8.5, VAPOR DIFFUSION, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.1 α = 79.19
b = 35.92 β = 82.66
c = 67.51 γ = 76.42
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-21
Diffraction Radiation
Monochromator Protocol
monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.98 NSLS X9B

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
1.25 25 89.0 -- 0.021 -- 2.0 75214 75214 0.0 -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)
1.25 1.29 55.0 -- 0.143 -- -- 4629

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 1.3 25.0 -- 1.0 69756 66305 3451 93.04 -- 0.15962 0.15778 0.19532 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 1.3 -- -- -- -- 0.188 0.204 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.846
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] -0.01
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.396
r_nbd_other 0.228
r_nbd_refined 0.316
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.098
r_dihedral_angle_3_deg 16.027
r_dihedral_angle_1_deg 6.081
r_angle_other_deg 0.875
r_angle_refined_deg 2.212
r_bond_other_d 0.0
r_bond_refined_d 0.006
r_xyhbond_nbd_refined 0.24
r_symmetry_vdw_refined 0.242
r_symmetry_vdw_other 0.22
r_symmetry_hbond_refined 0.319
r_mcbond_it 2.579
r_mcangle_it 3.64
r_scbond_it 3.405
r_scangle_it 4.947
r_rigid_bond_restr 1.578
r_sphericity_free 2.281
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2196
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 592

Software

Computing
Computing Package Purpose
DENZO 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
DENZO data collection