X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 295.0
Details 0.4 M Na/K Tartrate, 100 mM Na Phosphate/citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.54 α = 90
b = 90.7 β = 99.68
c = 74.52 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 160
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 a front end, vertically collimating premirror, double-crystal silicon (111) monochromator with a fixed-height exit beam, toroidal focusing mirror 2001-06-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.10030 ALS 5.0.2

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
1.8 50 95.4 -- -- -- -- 78342 77717 0.0 1000.0 --
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)
1.8 1.86 89.4 0.405 -- 3.1 -- --

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 1.8 19.99 -- 0.0 78342 67977 3639 91.99 0.207 0.18376 0.18167 0.22229 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 1.804 1.85 -- 234 4082 0.314 0.385 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.861
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.52
Anisotropic B[2][2] -0.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.23
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.515
r_scbond_it 3.122
r_mcangle_it 2.292
r_mcbond_it 1.436
r_symmetry_hbond_refined 0.35
r_symmetry_vdw_other 0.343
r_symmetry_vdw_refined 0.244
r_bond_refined_d 0.027
r_bond_other_d 0.003
r_angle_refined_deg 2.035
r_angle_other_deg 1.004
r_dihedral_angle_1_deg 5.776
r_chiral_restr 0.145
r_gen_planes_refined 0.011
r_gen_planes_other 0.004
r_nbd_refined 0.229
r_nbd_other 0.256
r_nbtor_other 0.09
r_xyhbond_nbd_refined 0.195
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6126
Nucleic Acid Atoms 0
Heterogen Atoms 178
Solvent Atoms 528

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMoRE model building
SCALEPACK data reduction
HKL-2000 data collection