9GA6 | pdb_00009ga6

The crystal structure of human Annexin A4 derived from crystals grown in 40 mM of CaCl2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZOC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.1 M sodium acetate (pH 4.6), 0.2 M ammonium sulfate, and 25 % (v/v) PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.742	α = 90
b = 39.906	β = 93.91
c = 73.456	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	PIXEL	DECTRIS EIGER2 X 9M		2022-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.991874	ESRF	ID30B

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	1.27	58.6	95.8	0.059	0.089	0.059	7.8	2.2		86437

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.27	1.29	91.7		0.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.27	58.6	86419	4312	95.599	0.175	0.1739	0.1831	0.1891	0.1953	11.972

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]
-0.002			0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.851
r_dihedral_angle_3_deg	11.381
r_dihedral_angle_2_deg	7.84
r_dihedral_angle_1_deg	6.039
r_lrange_it	5.391
r_lrange_other	5.355
r_scangle_it	4.018
r_scangle_other	3.974
r_scbond_it	2.92
r_scbond_other	2.774
r_angle_refined_deg	1.896
r_mcangle_other	1.877
r_mcangle_it	1.868
r_mcbond_it	1.285
r_mcbond_other	1.252
r_angle_other_deg	0.666
r_symmetry_nbd_refined	0.313
r_nbd_other	0.301
r_nbd_refined	0.255
r_symmetry_xyhbond_nbd_refined	0.213
r_nbtor_refined	0.185
r_symmetry_nbd_other	0.171
r_xyhbond_nbd_refined	0.124
r_xyhbond_nbd_other	0.1
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.072
r_metal_ion_refined	0.055
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2499
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing