X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details 0.2M ammonium sulfate, 0.1M bis-Tris pH 5.5, 25%(w/v) PEG 3350, vapor diffusion, hanging drop, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.92 α = 90
b = 82.48 β = 90
c = 135.28 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 3W1A 1.00000 BSRF 3W1A

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
2.03 19.84 90.3 0.079 -- -- -- -- 35757 -- -3.0 24.492
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)
2.03 2.16 83.8 0.346 -- 6.8 -- --

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 2.03 19.84 -- 0.0 -- 35757 1773 90.5 -- 0.194 0.191 0.254 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 2.034 2.087 -- 115 1767 0.431 0.499 -- 65.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 5.14
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.05
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 0.903
r_nbtor_refined 0.308
r_symmetry_vdw_refined 0.2
r_mcbond_it 0.541
r_chiral_restr 0.141
r_dihedral_angle_1_deg 7.538
r_xyhbond_nbd_refined 0.188
r_angle_refined_deg 2.182
r_nbd_refined 0.214
r_scbond_it 2.039
r_dihedral_angle_4_deg 19.463
r_bond_refined_d 0.023
r_gen_planes_refined 0.008
r_symmetry_hbond_refined 0.245
r_dihedral_angle_2_deg 45.183
r_scangle_it 3.266
r_dihedral_angle_3_deg 16.713
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3598
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 460

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.000
MAR345dtb data collection
XDS data reduction