2O3R | pdb_00002o3r

Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YH3	PDB entry 1YH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	300	100 mM MES, 15% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.724	α = 104.96
b = 52.999	β = 91.22
c = 65.937	γ = 94.57

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.976	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	30	95.2			54363	51754	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.81	82.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	THROUGHOUT	PDB entry 1YH3	1.75	20	49104	49104	2631	100	0.18528	0.18528	0.18298	0.25	0.22906	0.28	RANDOM	47.519

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]
-1.28	0.8	0.51	0.57	1.5	1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.978
r_dihedral_angle_4_deg	22.077
r_dihedral_angle_3_deg	18.574
r_dihedral_angle_1_deg	6.707
r_scangle_it	5.754
r_scbond_it	3.929
r_mcangle_it	2.498
r_angle_refined_deg	2.376
r_mcbond_it	1.706
r_nbtor_refined	0.321
r_nbd_refined	0.262
r_symmetry_hbond_refined	0.232
r_symmetry_vdw_refined	0.23
r_xyhbond_nbd_refined	0.204
r_chiral_restr	0.197
r_bond_refined_d	0.031
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4014
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing