5F21 | pdb_00005f21

human CD38 in complex with nanobody MU375

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, 25%(w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.149	α = 90
b = 69.666	β = 90
c = 123.476	γ = 90

Symmetry
Space Group	P 21 21 21

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		2012-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97852	SSRF	BL17U

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	1.9	50	99.3	0.069	10.6	6.1		31133

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	1.9	1.97	98.1		0.614		6.1	3022

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 (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	1YH3	1.9	50	28138	1499	94.53	0.165	0.1625	0.1716	0.2107	0.2167	RANDOM	27.244

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]
0.26			0.96		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.986
r_sphericity_free	24.384
r_dihedral_angle_4_deg	15.977
r_dihedral_angle_3_deg	13.588
r_dihedral_angle_1_deg	6.047
r_sphericity_bonded	4.15
r_angle_refined_deg	1.303
r_rigid_bond_restr	0.944
r_angle_other_deg	0.906
r_mcangle_it	0.883
r_mcbond_it	0.728
r_mcbond_other	0.722
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2855
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	16

Software

Software
Software Name	Purpose
Blu-Ice	data collection
DENZO	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
PHASER	phasing