X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 295.0
Details 15% PEG 8000, 20 mM Na acetate, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.52 α = 90
b = 83.52 β = 90
c = 114.45 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2002-01-13
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CAMD BEAMLINE GCPCC 1.069 CAMD GCPCC

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
3.3 30 99.4 -- 0.099 -- 4.5 6831 6831 -- -3.0 --
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)
3.3 3.42 99.9 -- 0.44 1.3 4.9 666

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 3.3 15.0 0.0 0.0 5815 5815 293 90.19 0.23 0.23 0.228 0.277 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 3.3 3.382 370 15 370 0.31 0.511 -- 80.88
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Anisotropic B[1][1] 2.51
Anisotropic B[1][2] 1.26
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.77
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 38.279
r_dihedral_angle_3_deg 20.328
r_symmetry_vdw_refined 0.199
r_chiral_restr 0.073
r_gen_planes_refined 0.003
r_nbtor_refined 0.327
r_dihedral_angle_4_deg 22.27
r_xyhbond_nbd_refined 0.135
r_mcangle_it 0.51
r_nbd_refined 0.236
r_scangle_it 1.183
r_dihedral_angle_1_deg 6.819
r_mcbond_it 0.272
r_scbond_it 0.684
r_angle_refined_deg 1.244
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1904
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 6

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
MAR345dtb data collection
HKL-2000 data reduction
HKL-2000 data scaling
AMoRE phasing