7NZC | pdb_00007nzc

First 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	2SRC	modified 2SRC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	0.2 M NaF, 22% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.4	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.962	α = 90
b = 35.962	β = 90
c = 181.333	γ = 120

Symmetry
Space Group	P 65 2 2

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 EIGER2 XE 16M	Monochromators	2019-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.11	30.7	96	0.999	26.1	19.4		2677

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	1.11	1.13			0.565	1.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	modified 2SRC	1.111	30.694	26656	1321	92.578	0.148	0.1468	0.15	0.1775	0.18	17.845

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]
0.043	0.022		0.043		-0.141

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.772
r_dihedral_angle_4_deg	31.468
r_mcangle_it	26.534
r_mcangle_other	26.493
r_lrange_it	26.469
r_lrange_other	26.451
r_scangle_it	24.836
r_scangle_other	24.809
r_scbond_it	18.746
r_scbond_other	18.745
r_mcbond_other	16.45
r_mcbond_it	16.418
r_dihedral_angle_3_deg	11.326
r_dihedral_angle_1_deg	7.622
r_rigid_bond_restr	3.128
r_angle_refined_deg	1.677
r_angle_other_deg	1.388
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_refined	0.208
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.17
r_nbd_other	0.155
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	502
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	15

Software

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