X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details 25-27% PEG 3350, 100mM Sodium acetate, 600mM LiCl, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.87 α = 90
b = 59.17 β = 100.77
c = 48.8 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2002-11-22
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 0.98045 APS 14-ID-B

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
1.35 16.61 89.8 -- 0.057 -- 4.6 -- 50130 -- -- --
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)
1.35 1.4 3.2 -- -- -- -- --

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
AB INITIO PHASING 1.35 16.61 -- -- 47586 47586 2545 99.75 -- 0.18033 0.17872 0.2103 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 1.349 1.384 -- 175 3422 0.309 0.38 -- 97.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.061
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.489
r_sphericity_free 8.741
r_rigid_bond_restr 2.148
r_scangle_it 3.115
r_scbond_it 2.566
r_mcangle_it 1.946
r_mcbond_other 0.622
r_mcbond_it 1.337
r_nbd_refined 0.221
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.083
r_dihedral_angle_4_deg 6.743
r_dihedral_angle_3_deg 11.227
r_dihedral_angle_2_deg 33.115
r_dihedral_angle_1_deg 5.886
r_angle_other_deg 1.711
r_angle_refined_deg 1.222
r_bond_other_d 0.001
r_bond_refined_d 0.008
r_nbd_other 0.182
r_nbtor_refined 0.175
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.121
r_metal_ion_refined 0.048
r_symmetry_vdw_refined 0.298
r_symmetry_vdw_other 0.252
r_symmetry_hbond_refined 0.087
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1798
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 286

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
REFMAC version: 5.2.0019 model building
HKL-2000 data collection