X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.2
Temperature 293.0
Details Crystallization components* AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM adenosine, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.74 α = 90
b = 66.7 β = 117.13
c = 88.56 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-12-07
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.96111 ESRF ID14-1

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
1.4 75.42 -- 0.099 0.099 -- 3.4 153897 153897 0.0 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)
1.4 1.48 59.3 0.452 0.452 1.6 2.3 --

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 1.4 74.54 -- -- 142874 142874 11010 100.0 -- 0.16906 0.16669 0.19908 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 1.4 1.436 -- 490 6229 0.285 0.324 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.611
Anisotropic B[1][1] 0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.08
Anisotropic B[2][2] -0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.013
r_symmetry_vdw_refined 0.259
r_mcbond_it 1.14
r_nbtor_other 0.083
r_gen_planes_refined 0.007
r_sphericity_bonded 2.386
r_angle_refined_deg 1.558
r_rigid_bond_restr 1.285
r_symmetry_hbond_refined 0.216
r_metal_ion_refined 0.018
r_nbd_refined 0.22
r_chiral_restr 0.087
r_bond_other_d 0.006
r_scangle_it 3.574
r_dihedral_angle_1_deg 5.791
r_gen_planes_other 0.002
r_sphericity_free 3.3
r_angle_other_deg 0.853
r_mcangle_it 1.68
r_scbond_it 2.368
r_nbd_other 0.259
r_xyhbond_nbd_refined 0.154
r_symmetry_vdw_other 0.299
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.046
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6590
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 1233

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
MOLREP phasing