3DZJ | pdb_00003dzj

Crystal structure of human CD38 extracellular domain E226Q mutant, NMN complex

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		6	298	100 mM MES pH 6.0, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.858	α = 106.11
b = 53.228	β = 91.97
c = 65.67	γ = 95.03

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		2006-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1		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	1.9	30	97.5	0.09	0.09	21.2	3.8		41633		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.98	95.2		0.436	0.436	2.9	2.9

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 (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	1.9	20	38959	38959	2061	100	0.188	0.185	0.24	0.241	0.28	RANDOM	33.29

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]
-1.06	0.56	0.45	0.65	0.98	1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.316
r_dihedral_angle_4_deg	17.826
r_dihedral_angle_3_deg	15.779
r_dihedral_angle_1_deg	6.39
r_scangle_it	4.537
r_scbond_it	2.975
r_mcangle_it	1.889
r_angle_refined_deg	1.772
r_mcbond_it	1.21
r_nbtor_refined	0.314
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.152
r_chiral_restr	0.129
r_symmetry_hbond_refined	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
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	4010
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	44

Software

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