7VKE | pdb_00007vke

Crystal structure of human CD38 ECD in complex with UniDab(TM) F11A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YH3	1YH3, 6PZW
experimental model	PDB	6PZW	1YH3, 6PZW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Sodium Citrate, PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.82	α = 90
b = 64.82	β = 90
c = 201.316	γ = 120

Symmetry
Space Group	P 32 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	PIXEL	DECTRIS EIGER X 16M		2020-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.79	49.08	100	0.083	0.999	12.1	10.1		47342

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.83			1.379	0.653

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1YH3, 6PZW	1.9	49.075	39716	1962	99.987	0.195	0.1927	0.2	0.2308	0.24	37.307

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]
0.102	0.051		0.102		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.475
r_dihedral_angle_4_deg	18.977
r_dihedral_angle_3_deg	15.041
r_lrange_it	8.512
r_lrange_other	8.409
r_dihedral_angle_1_deg	6.898
r_scangle_it	6.052
r_scangle_other	6.05
r_mcangle_it	4.764
r_mcangle_other	4.763
r_scbond_it	4.029
r_scbond_other	4.027
r_mcbond_other	3.208
r_mcbond_it	3.207
r_angle_other_deg	2.381
r_angle_refined_deg	1.6
r_symmetry_nbd_other	0.231
r_nbd_other	0.223
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_refined	0.212
r_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.164
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.057
r_bond_other_d	0.035
r_xyhbond_nbd_other	0.024
r_bond_refined_d	0.01
r_gen_planes_other	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3003
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing