X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 283.15
Details Peg 4000, Isopropanol, Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.99 α = 90
b = 54.99 β = 90
c = 115.78 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 2003-02-13
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.97626 BESSY 14.2

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
1.55 24.6 98.6 -- 0.051 -- 4.1 -- 26236 0.0 0.0 15.8
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)
1.55 1.59 98.3 -- 0.372 -- -- 1708

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 1.55 24.6 -- 2.0 26208 24319 1889 98.74 0.172 0.12779 0.12427 0.17388 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 1.551 1.591 1708 130 1730 0.133 0.217 0.07 98.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.456
Anisotropic B[1][1] -0.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.01
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.262
r_nbtor_other 0.08
r_sphericity_free 4.537
r_angle_other_deg 0.849
r_dihedral_angle_1_deg 7.767
r_scangle_it 5.169
r_chiral_restr 0.103
r_symmetry_vdw_refined 0.238
r_scbond_it 3.612
r_bond_refined_d 0.014
r_mcangle_it 3.266
r_nbd_refined 0.215
r_symmetry_vdw_other 0.244
r_angle_refined_deg 1.544
r_xyhbond_nbd_refined 0.134
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 2.414
r_rigid_bond_restr 2.122
r_sphericity_bonded 3.612
r_bond_other_d 0.002
r_symmetry_hbond_refined 0.184
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1508
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 294

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing