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_scangle_it 3.958
r_scbond_it 2.785
r_mcangle_it 3.118
r_mcbond_other 0.582
r_mcbond_it 2.285
r_nbd_refined 0.217
r_gen_planes_other 0.003
r_gen_planes_refined 0.007
r_chiral_restr 0.113
r_dihedral_angle_4_deg 19.188
r_dihedral_angle_3_deg 12.601
r_dihedral_angle_2_deg 35.841
r_dihedral_angle_1_deg 4.725
r_angle_other_deg 1.907
r_angle_refined_deg 1.742
r_bond_other_d 0.004
r_bond_refined_d 0.02
r_nbd_other 0.214
r_nbtor_refined 0.195
r_nbtor_other 0.13
r_xyhbond_nbd_refined 0.201
r_symmetry_vdw_refined 0.197
r_symmetry_vdw_other 0.314
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
EPMR model building