X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 298.0
Details 1.0M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.34 α = 90
b = 61.34 β = 90
c = 93.16 γ = 120
Symmetry
Space Group P 3 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 2003-01-24
Diffraction Radiation
Monochromator Protocol
Si (111) asymmetric cut, horizontal focus MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08, 1.282, 1.170, 1.283 SSRL BL7-1

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
1.3 50 91.3 0.04 -- -- 2.6 45526 45441 -- -3.0 16.442
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)
1.3 1.35 79.2 0.291 -- 2.4 2.0 3907

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
MAD 1.3 46.13 0.0 0.0 45437 43146 2291 95.0 0.1568 0.15686 0.15499 0.19316 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 1.302 1.336 3022 142 2880 0.249 0.273 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 19.986
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_metal_ion_refined 0.029
r_bond_refined_d 0.008
r_rigid_bond_restr 1.382
r_sphericity_free 10.447
r_bond_other_d 0.002
r_gen_planes_refined 0.005
r_symmetry_vdw_other 0.272
r_angle_other_deg 0.78
r_mcangle_it 4.959
r_scbond_it 5.181
r_gen_planes_other 0.001
r_nbd_refined 0.195
r_nbd_other 0.25
r_symmetry_vdw_refined 0.138
r_symmetry_hbond_refined 0.07
r_nbtor_other 0.08
r_mcbond_it 3.824
r_dihedral_angle_1_deg 6.234
r_sphericity_bonded 8.019
r_scangle_it 6.55
r_angle_refined_deg 1.242
r_chiral_restr 0.082
r_xyhbond_nbd_refined 0.101
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1250
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 194

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing