3P5S | pdb_00003p5s

Structural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GC6	PDB entry 3GC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20-30% PEG 4000, 50-250 mM AMMONIUM SULFATE, 100 MM SODIUM CACODYLATE OR SODIUM ACETATE OR MES AT PH-6.0-6.5, pH 6.0 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.205	α = 90
b = 80.029	β = 90
c = 157.725	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	130	CCD	ADSC QUANTUM 315r	could not see them	2007-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	78.8	90	0.084	1	2.9	110000	39086	1	1	26

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	random throughout, test set	PDB entry 3GC6	1.95	40.014	1	39086	37543	2902	86.15	0.209	0.2053	0.2	0.2515	0.24	random

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-5.467			1.5643		3.9028

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.888
f_angle_d	1.192
f_chiral_restr	0.079
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3753
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	108

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PHENIX	model building
ELVES	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.