X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP with 2 mM CdCl2 Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M HEPES, pH7.0 with 10 mM 2, 5-di-O-Bn-InsP4, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.11 α = 90
b = 111.13 β = 90
c = 41.3 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 MARMOSAIC 225 mm CCD -- 2013-07-27
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.9 50 99.9 -- 0.073 -- 7.2 33324 33324 3.0 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)
1.9 1.93 99.6 -- 0.46 3.7 6.4 1612

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
FOURIER SYNTHESIS 1.9 35.53 -- 0.0 31228 31228 2036 99.58 0.1812 0.1812 0.179 0.21542 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 1.9 1.945 -- 139 2171 0.222 0.268 -- 95.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 27.166
Anisotropic B[1][1] 0.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.39
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.0
r_dihedral_angle_2_deg 37.386
r_angle_other_deg 3.541
r_scangle_other 3.716
r_long_range_B_refined 7.215
r_chiral_restr 0.094
r_scbond_it 2.348
r_dihedral_angle_4_deg 15.108
r_gen_planes_refined 0.006
r_mcbond_it 1.823
r_dihedral_angle_3_deg 13.774
r_mcbond_other 1.823
r_mcangle_other 3.0
r_gen_planes_other 0.009
r_bond_refined_d 0.01
r_dihedral_angle_1_deg 5.554
r_angle_refined_deg 1.545
r_mcangle_it 3.001
r_long_range_B_other 6.964
r_scbond_other 2.347
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2604
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 342

Software

Software
Software Name Purpose
HKL-2000 data collection
CCP4 model building
REFMAC refinement version: 5.7.0032
HKL-2000 data reduction
HKL-2000 data scaling
CCP4 phasing