7L97 | pdb_00007l97

Crystal structure of STAMBPL1 in complex with an engineered binder

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZNR	2ZNR,1UBQ
experimental model	PDB	1UBQ	2ZNR,1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20% PEG 1500, 0.2M NaCl, 0.1M HEPES pH7.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.709	α = 90
b = 68.882	β = 98.51
c = 57.329	γ = 90

Symmetry
Space Group	C 1 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 PILATUS3 S 6M		2016-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2	50	99	0.123	0.139	0.063	7.2	4.4		16078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	96.4		0.7	0.814	0.405	0.769		3.4

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2ZNR,1UBQ	2.01	50	15388	690	98.49	0.1859	0.1846	0.2137	0.2263	RANDOM	37.279

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]
-0.82		-0.27	3.7		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.189
r_dihedral_angle_4_deg	16.555
r_dihedral_angle_3_deg	12.432
r_dihedral_angle_1_deg	6.439
r_angle_refined_deg	1.377
r_angle_other_deg	0.881
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1954
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	22

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction