X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 293.0
Details 5% PEG 6000, 0.1M citric acid, pH 4.0, Vapor diffusion, hanging drop, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.48 α = 90
b = 64.92 β = 90
c = 103.94 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 Bruker DIP-6040 -- 2004-04-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU -- SPring-8 BL44XU

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
1.92 10 92.5 -- -- -- -- -- 17451 -- -- 27.95

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 1.92 10.0 -- -- -- 17451 948 92.47 -- 0.20211 0.2 0.25 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 1.92 1.968 -- 47 841 0.199 0.277 -- 62.45
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.821
Anisotropic B[1][1] -0.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.08
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.189
r_dihedral_angle_3_deg 16.799
r_gen_planes_refined 0.009
r_dihedral_angle_2_deg 34.059
r_nbtor_refined 0.303
r_xyhbond_nbd_refined 0.183
r_chiral_restr 0.3
r_nbd_refined 0.22
r_angle_refined_deg 2.208
r_symmetry_hbond_refined 0.084
r_dihedral_angle_4_deg 23.676
r_bond_refined_d 0.016
r_mcangle_it 2.061
r_scangle_it 4.599
r_dihedral_angle_1_deg 6.064
r_mcbond_it 1.286
r_scbond_it 2.944
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2042
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 205

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
MOSFLM data reduction
SCALA data scaling