X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details PEG 8000, Mg acetate, MPD, ADA buffer, pH 6.2, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.11 α = 90
b = 79.11 β = 90
c = 107.1 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.54 -- --

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
1.7 68.52 98.5 0.044 0.044 -- 17.2 22282 22282 -- -- --
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)
1.7 1.79 90.8 0.142 0.142 4.9 15.5 2918

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 1.7 21.1 -- 0.0 -- 22238 1136 99.48 -- 0.1827 0.1816 0.2033 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 1.701 1.745 -- 88 1451 0.264 0.297 -- 96.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.3
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] -0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.213
r_dihedral_angle_4_deg 8.45
r_chiral_restr 0.096
r_bond_refined_d 0.011
r_mcangle_it 1.09
r_scangle_it 2.849
r_dihedral_angle_2_deg 35.064
r_nbtor_refined 0.311
r_gen_planes_refined 0.007
r_xyhbond_nbd_refined 0.134
r_dihedral_angle_1_deg 6.201
r_angle_refined_deg 1.442
r_dihedral_angle_3_deg 13.168
r_symmetry_hbond_refined 0.097
r_mcbond_it 0.694
r_nbd_refined 0.188
r_scbond_it 1.815
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1272
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 133

Software

Software
Software Name Purpose
MOSFLM data reduction version: 3.2.17
SCALA data scaling version: 3.2.17
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10