X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details spermine, potassium chloride, MPD, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.01 α = 90
b = 35.01 β = 90
c = 22.26 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-08-20
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.8985 APS 14-BM-D

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
1.1 16.55 95.3 -- 0.037 -- 20.0 -- 5690 0.0 0.0 --
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)
1.1 1.14 71.9 -- 0.088 -- -- 770

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 1.1 16.55 -- 2.0 -- 5382 308 94.82 -- 0.12733 0.12678 0.13607 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 1.1 1.16 -- 34 589 0.08 0.11 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 6.497
Anisotropic B[1][1] -0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.53
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.032
r_rigid_bond_restr 0.855
r_bond_refined_d 0.01
r_angle_other_deg 2.098
r_scangle_it 2.065
r_chiral_restr 0.123
r_sphericity_free 8.627
r_symmetry_vdw_refined 0.752
r_nbd_refined 0.412
r_angle_refined_deg 1.607
r_bond_other_d 0.003
r_symmetry_vdw_other 0.346
r_sphericity_bonded 2.673
r_symmetry_hbond_refined 0.099
r_nbtor_other 0.096
r_scbond_it 1.539
r_xyhbond_nbd_refined 0.121
r_nbd_other 0.196
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 162
Heterogen Atoms 3
Solvent Atoms 90

Software

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