X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details METHOD: HANGING-DROP, VAPOUR-DIFFUSION PROTEIN CONCENTRATION: 8 MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 50% MPD, 15% ETHANOL, 0.01 M NA2 ACETATE, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.24 α = 90
b = 52.19 β = 90
c = 58.1 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 MARRESEARCH 2 AU COATED X-RAY MIRRORS 2004-05-17
Diffraction Radiation
Monochromator Protocol
ROEMO TYPE DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 -- MPG/DESY, HAMBURG BW6

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
1.45 30 98.4 0.04 -- -- 3.3 -- 16143 -- 0.0 --
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)
1.45 1.48 97.0 0.31 -- 3.7 2.9 --

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 1.45 20.03 -- -- -- 16142 879 98.5 -- 0.15 0.149 0.17 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 1.45 1.49 -- 67 1069 0.176 0.227 -- 95.62
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.3
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.742
r_angle_other_deg 1.907
r_scbond_it 2.785
r_scangle_it 3.958
r_chiral_restr 0.113
r_mcbond_it 2.285
r_bond_other_d 0.004
r_mcangle_it 3.118
r_nbtor_other 0.13
r_nbd_other 0.214
r_gen_planes_refined 0.007
r_symmetry_vdw_other 0.314
r_mcbond_other 0.582
r_dihedral_angle_3_deg 12.601
r_nbd_refined 0.217
r_gen_planes_other 0.003
r_nbtor_refined 0.195
r_dihedral_angle_1_deg 4.725
r_symmetry_vdw_refined 0.197
r_bond_refined_d 0.02
r_dihedral_angle_2_deg 35.841
r_dihedral_angle_4_deg 19.188
r_xyhbond_nbd_refined 0.201
r_symmetry_hbond_refined 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 871
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 103

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
EPMR phasing