X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.95 α = 90
b = 102.95 β = 90
c = 41.83 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
2.2 40 98.9 0.056 -- -- 7.3 -- 13367 -- -- 49.98
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)
2.2 2.24 97.1 0.044 -- 3.55 6.7 --

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 2.2 40.0 -- -- -- 12946 1281 99.0 -- 0.23 0.223 0.291 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 2.2 2.26 -- 93 861 0.305 0.383 -- 99.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.99
Anisotropic B[1][1] -5.017
Anisotropic B[1][2] -2.508
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.017
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.525
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.463
r_xyhbond_nbd_refined 0.166
r_dihedral_angle_2_deg 36.723
r_dihedral_angle_1_deg 9.426
r_symmetry_vdw_refined 0.211
r_mcangle_it 0.75
r_scbond_it 1.369
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 5.47
r_chiral_restr 0.08
r_scangle_it 1.926
r_symmetry_hbond_refined 0.118
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 16.163
r_angle_refined_deg 1.573
r_nbd_refined 0.205
r_nbtor_refined 0.304
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1626
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 96

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