X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 3.5
Temperature 277.0
Details 60% (v/v) MPD, Hepes 15 mM pH 7.0, 1 mM Ac2Cu, Counter-diffusion, temperature 277K, pH 3.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.51 α = 90
b = 103.51 β = 90
c = 41.4 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2005-02-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM16 -- ESRF BM16

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
2.25 40 99.0 0.059 -- -- 7.1 -- 12290 -- -- 47.21
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)
2.25 2.29 95.5 0.352 -- 3.69 6.1 --

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 2.25 40.0 -- -- -- 12128 586 99.1 0.227 0.227 0.225 0.268 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 2.25 2.31 -- 41 829 0.32 0.49 -- 98.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.84
Anisotropic B[1][1] -4.981
Anisotropic B[1][2] -2.491
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.981
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.472
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.184
r_gen_planes_refined 0.005
r_dihedral_angle_2_deg 36.288
r_dihedral_angle_4_deg 24.163
r_dihedral_angle_3_deg 15.364
r_chiral_restr 0.091
r_mcbond_it 0.537
r_nbd_refined 0.212
r_bond_refined_d 0.013
r_mcangle_it 0.975
r_dihedral_angle_1_deg 6.425
r_scangle_it 2.616
r_xyhbond_nbd_refined 0.452
r_symmetry_hbond_refined 0.198
r_angle_refined_deg 1.518
r_scbond_it 1.929
r_nbtor_refined 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1626
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 80

Software

Software
Software Name Purpose
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement version: refmac_5.2.0019
PDB_EXTRACT data extraction version: 1.700
MOSFLM data reduction
HKL-2000 data scaling
Coot model building
MolProbity model building