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 AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000 , pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 M solution of NaBr

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.5 α = 90
b = 92.62 β = 90
c = 138.25 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Torodial mirror 2002-05-08
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.91957, 0.9204, 0.88561 EMBL/DESY, Hamburg X31

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 20 98.2 0.092 0.092 -- 4.17 32466 32466 0.0 0.0 24.13
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 2.23 96.6 0.33 -- 3.9 3.3 1272

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
MAD 2.2 19.32 0.0 0.0 30818 30818 1648 98.3 0.19069 0.19069 0.18855 0.23111 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 2.257 1151 121 2255 0.198 0.26 -- 96.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.068
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.186
r_angle_refined_deg 1.901
r_mcbond_it 1.186
r_nbd_refined 0.218
r_symmetry_vdw_refined 0.203
r_xyhbond_nbd_refined 0.168
r_symmetry_hbond_refined 0.306
r_chiral_restr 0.131
r_scangle_it 5.264
r_gen_planes_refined 0.009
r_bond_refined_d 0.027
r_mcangle_it 2.031
r_scbond_it 3.392
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.092
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3286
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 380

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE_RESOLVE model building
REFMAC refinement version: 5.1.24
SOLVE phasing
RESOLVE phasing