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 cacodylate, sodium acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.77 α = 90
b = 107.4 β = 90
c = 270.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-11-26
Diffraction Radiation
Monochromator Protocol
SI 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B -- PHOTON FACTORY BL-18B

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 40 98.7 0.108 -- -- 7.4 -- 183404 -- -- --
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 2.0 92.1 0.305 -- 2.4 4.4 --

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 1.9 36.0 -- -- -- 174100 9195 98.69 -- 0.169 0.16747 0.19791 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 1.949 -- 593 11476 0.206 0.244 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.102
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.04
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.228
r_gen_planes_other 0.002
r_symmetry_hbond_refined 0.209
r_mcbond_it 0.59
r_scbond_it 1.747
r_angle_refined_deg 1.321
r_angle_other_deg 0.759
r_xyhbond_nbd_other 0.151
r_mcangle_it 1.089
r_gen_planes_refined 0.005
r_symmetry_vdw_refined 0.284
r_symmetry_vdw_other 0.174
r_bond_other_d 0.001
r_chiral_restr 0.086
r_dihedral_angle_3_deg 17.32
r_nbd_other 0.196
r_dihedral_angle_1_deg 4.131
r_scangle_it 2.866
r_xyhbond_nbd_refined 0.137
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17780
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1475

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
AMORE model building
REFMAC version: 5.0 refinement