9GOX | pdb_00009gox

Crystal structure of Fab B6-D9 in complex with CD38

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DUN
experimental model	PDB	7DHA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	7 % v/v T-mate pH 7.0, 0.1 M HEPES pH 7.2, 20 % v/v PEG Smear Medium (BCS screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.045	α = 90
b = 166.045	β = 90
c = 78.769	γ = 90

Symmetry
Space Group	P 43 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	80	PIXEL	DECTRIS EIGER2 X 16M		2022-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.84	71.27	77	0.136	0.136	0.143	12.2	11.4		73151			34.964

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.843	2.02	68.8		1.64		12.8

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	1.84	71.27	69483	3668	76.98	0.17616	0.17443	0.1816	0.20831	0.2123	RANDOM	34.964

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]
0.01			0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.112
r_dihedral_angle_4_deg	19.447
r_dihedral_angle_3_deg	13.889
r_dihedral_angle_1_deg	7.599
r_long_range_B_refined	6.258
r_long_range_B_other	6.09
r_scangle_other	3.782
r_mcangle_it	2.874
r_mcangle_other	2.874
r_scbond_it	2.437
r_scbond_other	2.437
r_mcbond_it	1.856
r_mcbond_other	1.851
r_angle_refined_deg	1.426
r_angle_other_deg	1.216
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5341
Nucleic Acid Atoms
Solvent Atoms	696
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data reduction
autoPROC	data scaling
Aimless	data scaling
MOLREP	phasing