1DJ9

CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 289.0
Details AMMONIUM SULPHATE, SODIUM CHLORIDE, BIS-TRIS PROPANE BUFFER, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.89 α = 90
b = 58.89 β = 90
c = 201.77 γ = 120
Symmetry
Space Group P 31 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX7.2 -- SRS PX7.2

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
1.99 31.62 99.3 0.065 -- -- 2.9 28007 27822 0.0 0.0 37.0
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)
1.99 2.06 93.5 0.452 -- -- 2.7 --

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
AB INITIO 2.0 10.0 0.0 0.0 27177 27314 820 99.5 0.212 0.212 0.212 0.278 RANDOM
RMS Deviations
Key Refinement Restraint Deviation
s_approx_iso_adps 0.0
s_similar_adp_cmpnt 0.1
s_rigid_bond_adp_cmpnt 0.0
s_anti_bump_dis_restr 0.0
s_non_zero_chiral_vol 0.03
s_zero_chiral_vol 0.03
s_from_restr_planes 0.025
s_similar_dist 0.0
s_angle_d 0.02
s_bond_d 0.007
Coordinate Error
Parameter Value
Occupancy Sum Hydrogen 0.0
Occupancy Sum Non Hydrogen 3208.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2912
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 337

Software

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
SHELXL-97 Structure Refinement
Software
Software Name Purpose
SHELXL-97 refinement
X-PLOR model building