X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details 20% Peg 4k, 150mM Na Formate, and 100 mM Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.69 α = 90
b = 55.64 β = 90
c = 88.69 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
IMAGE PLATE MARRESEARCH -- 1999-03-30
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 1.08 SSRL BL9-1

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
1.75 28.7 98.3 0.04 -- -- 7.0 225846 222007 -3.0 -3.0 30.1
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)
1.75 1.77 97.5 0.552 -- 1.7 -- 826

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 1.75 47.0 0.0 0.0 25836 24317 1235 98.39 0.20499 0.20499 0.20304 0.24524 RANDOM within shells
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 1.75 1.795 -- 87 1767 0.259 0.388 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.285
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.018
r_scbond_it 2.609
r_symmetry_vdw_refined 0.377
r_nbd_other 0.211
r_nbd_refined 0.246
r_dihedral_angle_3_deg 19.044
r_xyhbond_nbd_refined 0.225
r_angle_other_deg 1.218
r_gen_planes_refined 0.007
r_symmetry_vdw_other 0.235
r_scangle_it 4.144
r_bond_refined_d 0.017
r_gen_planes_other 0.006
r_angle_refined_deg 1.803
r_mcbond_it 1.023
r_chiral_restr 0.146
r_mcangle_it 1.776
r_symmetry_hbond_refined 0.456
r_bond_other_d 0.001
r_nbtor_other 0.621
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1691
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 153

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing