5BNI | pdb_00005bni

Porcine CD38 complexed with complexed with a covalent intermediate, ribo-F-ribose-5'-phosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	PEG 4000, PEG 400, magnesium chloride, tris

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.507	α = 90
b = 104.973	β = 90
c = 63.785	γ = 90

Symmetry
Space Group	P 21 21 2

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 315r		2011-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	30	96	0.134	4.5	3.9		16205

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	2.5	2.59	95.5		0.637		3.5	1569

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.5	25	15278	819	96.04	0.1915	0.1869	0.1857	0.2776	0.2781	RANDOM	54.036

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]
-3.07			0.72		2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.462
r_dihedral_angle_2_deg	39.205
r_dihedral_angle_3_deg	22.275
r_sphericity_bonded	21.308
r_dihedral_angle_4_deg	17.881
r_rigid_bond_restr	12.019
r_dihedral_angle_1_deg	2.303
r_angle_refined_deg	1.443
r_chiral_restr	0.091
r_bond_refined_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.462
r_dihedral_angle_2_deg	39.205
r_dihedral_angle_3_deg	22.275
r_sphericity_bonded	21.308
r_dihedral_angle_4_deg	17.881
r_rigid_bond_restr	12.019
r_dihedral_angle_1_deg	2.303
r_angle_refined_deg	1.443
r_chiral_restr	0.091
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3701
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	35

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.