5G4P

Crystal structure of human hippocalcin at 2.4 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.5, 18% V/V 2-PROPANOL, 16% W/V PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.38	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.97	α = 90
b = 50.97	β = 90
c = 284.582	γ = 120

Symmetry
Space Group	P 61

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	MIRRORS	2016-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.42	43.56	98.8	0.04	11.07	3.3		15734			63.7

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	2.42	2.59	99.9		0.62	1.8	3.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 5AEQ	2.42	47.43	14886	770	98.82	0.22766	0.22519	0.27685	RANDOM	78.609

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]
-2.56	-1.28		-2.56		8.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.431
r_dihedral_angle_3_deg	17.349
r_dihedral_angle_4_deg	17.27
r_long_range_B_refined	8.803
r_long_range_B_other	8.803
r_dihedral_angle_1_deg	6.451
r_scbond_it	3.324
r_scbond_other	3.323
r_mcangle_it	3.181
r_mcangle_other	3.18
r_scangle_other	2.668
r_mcbond_other	2.481
r_mcbond_it	2.48
r_angle_refined_deg	1.562
r_angle_other_deg	1.044
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2972
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing