X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 0.1 M Tris, 60% AS, 5 mM Zinc Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.35 α = 90
b = 77.35 β = 90
c = 80.05 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-07-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.9795 APS 22-ID

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
2.3 20 99.2 0.041 -- -- 8.5 12703 12596 0.0 -3.0 34.0
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)
2.3 2.35 89.8 0.102 -- 12.8 9.5 757

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
FOURIER SYNTHESIS 2.3 10.0 -- 0.0 11839 11839 607 100.0 0.16505 0.16505 0.16181 0.22532 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 2.3 2.361 -- 52 824 0.161 0.296 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.198
Anisotropic B[1][1] -1.84
Anisotropic B[1][2] -0.92
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.77
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 8.163
r_scangle_it 14.042
r_gen_planes_refined 0.006
r_xyhbond_nbd_refined 0.153
r_symmetry_vdw_refined 0.242
r_scbond_it 12.079
r_nbd_refined 0.244
r_symmetry_hbond_refined 0.226
r_angle_refined_deg 1.623
r_dihedral_angle_3_deg 16.21
r_chiral_restr 0.11
r_bond_refined_d 0.017
r_dihedral_angle_1_deg 4.879
r_mcbond_it 5.293
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1802
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 188

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
CCP4 model building
REFMAC refinement version: 5.0
HKL-2000 data reduction
CCP4 phasing