7NZD | pdb_00007nzd

Fourth SH3 domain of POSH (Plenty of SH3 Domains protein)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2LJ1	Homology model build with the template 2LJ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	0.1M MES pH 6.5, 23% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.6	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.52	α = 90
b = 45.52	β = 90
c = 65.74	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 PILATUS 6M-F		2020-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.45	65.74	100	1	23.8	18.8		14475

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.48	99.29		0.52	1

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	Homology model build with the template 2LJ1	1.45	65.74	14443	716	99.841	0.164	0.1601	0.17	0.2275	0.22	37.451

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]
1.274	0.637		1.274		-4.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.278
r_dihedral_angle_4_deg	21.083
r_dihedral_angle_3_deg	13.301
r_dihedral_angle_1_deg	6.829
r_lrange_it	6.782
r_lrange_other	6.778
r_scangle_it	6.603
r_scangle_other	6.595
r_scbond_it	5.426
r_scbond_other	5.419
r_rigid_bond_restr	4.449
r_mcangle_it	4.05
r_mcangle_other	4.048
r_mcbond_it	3.584
r_mcbond_other	3.342
r_angle_refined_deg	1.501
r_angle_other_deg	1.305
r_symmetry_nbd_refined	0.461
r_nbd_other	0.307
r_xyhbond_nbd_refined	0.245
r_symmetry_nbd_other	0.196
r_nbd_refined	0.192
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	511
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing