3F6Y | pdb_00003f6y

Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium

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	7.5	300	10% PEG 4000, 100mM MES, 100mM calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.687	α = 90
b = 60.058	β = 129.69
c = 56.932	γ = 90

Symmetry
Space Group	C 1 2 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		2006-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.978	CHESS	A1

Data Collection

Overall
ID #	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	1.45	30	91.5	0.044	0.044	25.28	3.3	39005	35690	1.4	2.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.45	1.5	52.6		0.326	2.08	1.7

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	1.45	20	36972	33844	1809	91.54	0.1482	0.1482	0.14624	0.15	0.18416	0.19	RANDOM	21.359

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]
-0.06		-0.29	-0.18		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.449
r_dihedral_angle_4_deg	12.791
r_dihedral_angle_3_deg	11.382
r_dihedral_angle_1_deg	6.036
r_scangle_it	4.855
r_scbond_it	3.404
r_mcangle_it	2.431
r_mcbond_it	1.552
r_angle_refined_deg	1.326
r_nbtor_refined	0.313
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.213
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.091
r_symmetry_metal_ion_refined	0.05
r_metal_ion_refined	0.042
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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	1870
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	3

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling