9BAR | pdb_00009bar

Crystal structure of the alpha parvalbumin from thornback ray

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZH6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	2.5 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
1.72	28.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.199	α = 90
b = 37.725	β = 95.369
c = 38.809	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RAYONIX MX300-HS		2021-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	40	95	0.091	0.091	0.108	0.058	0.999	18.7	3.4		9078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78			0.392	0.392	0.478	0.259	0.85	2.2

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	PDB entry 5ZH6	1.75	32.078	9019	415	95.037	0.184	0.1824	0.1933	0.2228	0.2369	17.19

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]
-1.577		-0.356	0.642		0.985

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.319
r_dihedral_angle_3_deg	11.034
r_dihedral_angle_2_deg	7.82
r_dihedral_angle_1_deg	5.672
r_lrange_it	5.081
r_lrange_other	4.619
r_scangle_other	2.355
r_scangle_it	2.353
r_mcangle_it	1.57
r_mcangle_other	1.569
r_scbond_it	1.385
r_scbond_other	1.379
r_angle_refined_deg	1.264
r_mcbond_it	0.949
r_mcbond_other	0.948
r_angle_other_deg	0.491
r_symmetry_xyhbond_nbd_refined	0.232
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.227
r_nbd_other	0.218
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.162
r_metal_ion_refined	0.133
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.066
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	821
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling
MOLREP	phasing