X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.75
Temperature 298.0
Details 0.2M Zinc Acetate, 0.2M Imidazole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.17 α = 90
b = 69.64 β = 90
c = 120.65 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Capillary optics (AXCO) 2006-03-24
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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
2.03 60.3 98.71 0.044 -- -- 3.2 -- 13365 -- 5.6 --
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)
2.03 2.1 96.1 0.204 -- 3.1 3.1 1357

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 2.03 50.0 2.0 -- -- 13365 710 98.71 -- 0.19441 0.19201 0.24108 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 2.034 2.086 1014 49 965 0.214 0.255 -- 98.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.253
Anisotropic B[1][1] -0.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.99
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.2
r_mcangle_it 1.624
r_nbtor_refined 0.296
r_dihedral_angle_3_deg 15.074
r_symmetry_vdw_refined 0.235
r_symmetry_hbond_refined 0.362
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 4.209
r_dihedral_angle_2_deg 34.358
r_metal_ion_refined 0.089
r_scangle_it 3.658
r_xyhbond_nbd_refined 0.198
r_angle_refined_deg 1.194
r_dihedral_angle_4_deg 18.131
r_mcbond_it 0.967
r_chiral_restr 0.086
r_scbond_it 2.363
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1357
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 120

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing