5F1K | pdb_00005f1k

human CD38 in complex with nanobody MU1053

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	8	298	0.1M Tris, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.552	α = 90
b = 96.242	β = 90
c = 133.777	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		2012-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	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	2.3	50	99.7	0.092	9.7	9.8		51358

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	2.3	2.38	100		0.576		9.1	5075

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	2.3	50	42953	2259	87.75	0.1996	0.198	0.2042	0.2313	0.2334	RANDOM	42.654

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]
-2.59			0.37		2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.191
r_sphericity_free	30.549
r_dihedral_angle_4_deg	20.424
r_dihedral_angle_3_deg	14.514
r_dihedral_angle_1_deg	5.765
r_sphericity_bonded	3.163
r_rigid_bond_restr	1.459
r_angle_refined_deg	1.383
r_angle_other_deg	1.181
r_mcangle_it	0.658
r_mcbond_it	0.507
r_mcbond_other	0.507
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5755
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
HKL-2000	data processing