X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 10.4
Temperature 293.0
Details 0.1 M CAPS pH 10.4, 18% PEG 3350, 3% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.05 α = 90
b = 108.05 β = 90
c = 78.56 γ = 90
Symmetry
Space Group P 42

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 Mirrors 2006-02-12
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-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
2.1 50 99.9 0.063 -- -- 7.7 52686 52686 -- -3.0 36.6
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)
2.1 2.15 99.9 0.364 -- 5.9 7.0 --

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 2.1 15.0 -- 0.0 49847 49847 2674 94.7 0.212 0.212 0.208 0.283 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 2.1 2.153 -- 198 3636 0.238 0.327 -- 99.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.9
Anisotropic B[1][1] -0.84
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.68
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 34.906
r_symmetry_vdw_refined 0.259
r_dihedral_angle_4_deg 18.316
r_scangle_it 15.056
r_chiral_restr 0.129
r_nbd_refined 0.224
r_angle_refined_deg 1.81
r_symmetry_hbond_refined 0.208
r_scbond_it 13.526
r_mcbond_it 5.871
r_dihedral_angle_3_deg 18.362
r_xyhbond_nbd_refined 0.156
r_nbtor_refined 0.313
r_mcangle_it 8.551
r_dihedral_angle_1_deg 7.395
r_gen_planes_refined 0.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.241
Luzzati ESD (R-Free Set) 0.222
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6468
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 270

Software

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