X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 0.2M Na Acetate, 13.75% PEG 4000, 0.1M Hepes pH7.0, 1mM F6P, 2mM MnCl2, 1mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.87 α = 90
b = 73.45 β = 106.3
c = 78.03 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC mirrors 1999-04-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.15 40.26 93.8 0.106 -- -- -- -- 32736 -- -3.0 --
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)
2.15 2.23 64.5 0.483 -- 2.44 2.3 2255

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 2.15 40.26 -- 0.0 32734 32734 1639 93.62 0.19582 0.19582 0.19269 0.25514 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 2.15 2.21 -- 81 1464 0.226 0.297 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.619
Anisotropic B[1][1] 0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.12
Anisotropic B[2][2] -0.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.84
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.003
r_xyhbond_nbd_refined 0.148
r_gen_planes_refined 0.013
r_xyhbond_nbd_other 0.073
r_mcbond_it 2.49
r_nbd_refined 0.244
r_gen_planes_other 0.007
r_dihedral_angle_3_deg 23.573
r_nbtor_other 0.106
r_scbond_it 4.894
r_chiral_restr 0.168
r_nbd_other 0.25
r_symmetry_vdw_other 0.422
r_angle_refined_deg 3.04
r_scangle_it 7.059
r_dihedral_angle_1_deg 5.056
r_symmetry_vdw_refined 0.366
r_symmetry_hbond_refined 0.242
r_angle_other_deg 1.661
r_bond_refined_d 0.02
r_mcangle_it 4.295
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4767
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 106

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.0