9BB8 | pdb_00009bb8

Crystal structure of human alpha parvalbumin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RTP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	3.4 M sodium malonate, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.112	α = 90
b = 83.112	β = 90
c = 31.192	γ = 90

Symmetry
Space Group	P 43 21 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 EIGER X 16M		2023-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	2.72	37.169	95.5	0.096	0.096	0.112	0.055	0.991	11.6	3.5		3079

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	2.72	2.77	99.4		0.471	0.471	0.546	0.264	0.767	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 1RTP	2.722	37.169	3070	145	95.639	0.208	0.2054	0.2049	0.2551	0.2592	42.844

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]
-0.452			-0.452		0.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_6_deg	10.777
r_dihedral_angle_2_deg	7.564
r_lrange_it	5.237
r_lrange_other	5.227
r_dihedral_angle_1_deg	5.177
r_scangle_it	2.985
r_scangle_other	2.982
r_mcangle_it	2.105
r_mcangle_other	2.104
r_scbond_it	1.77
r_scbond_other	1.768
r_angle_refined_deg	1.375
r_mcbond_it	1.299
r_mcbond_other	1.297
r_angle_other_deg	0.491
r_metal_ion_refined	0.29
r_symmetry_nbd_other	0.221
r_nbd_refined	0.215
r_nbd_other	0.206
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.152
r_xyhbond_nbd_refined	0.137
r_symmetry_nbd_refined	0.103
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.061
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	831
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	2

Software

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