X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details PEG 8000, 0.1M MES, 0.2M Zn(OAc)2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.21 α = 90
b = 73.5 β = 96.33
c = 130.48 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2002-04-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.95369 SSRL BL11-1

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
2.65 40 97.5 -- 0.07 -- 3.5 28609 27894 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)
2.65 2.71 91.8 -- 0.76 1.8 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
MOLECULAR REPLACEMENT 2.65 40.0 -- -- 26296 24442 1238 92.95 -- 0.21494 0.21312 0.2496 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 2.65 2.719 -- 62 1452 0.365 0.378 -- 75.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 94.943
Anisotropic B[1][1] 4.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.14
Anisotropic B[2][2] 0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.42
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 20.535
r_mcbond_it 0.489
r_dihedral_angle_1_deg 7.163
r_symmetry_hbond_refined 0.298
r_scangle_it 1.871
r_angle_refined_deg 1.431
r_metal_ion_refined 0.215
r_scbond_it 1.22
r_dihedral_angle_2_deg 34.942
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.157
r_symmetry_vdw_refined 0.26
r_symmetry_metal_ion_refined 0.145
r_nbtor_refined 0.309
r_bond_refined_d 0.014
r_chiral_restr 0.092
r_nbd_refined 0.22
r_dihedral_angle_3_deg 19.431
r_mcangle_it 0.878
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6668
Nucleic Acid Atoms 0
Heterogen Atoms 11
Solvent Atoms 27

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
ADSC data collection
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing