2J5W

Ceruloplasmin revisited: structural and functional roles of various metal cation binding sites

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		PH 4.5

Crystal Properties
Matthews coefficient	Solvent content
4.27	71.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.14	α = 90
b = 209.139	β = 90
c = 82.752	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.8	75.3	100	0.07	6.4	3.7		51383		2

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	2.8	2.95	100		0.32	3.8	3.8

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 1KCW	2.8	68.52	48754	2608	100	0.177	0.175	0.226	RANDOM	40.93

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]
-0.04	-0.02		-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.437
r_dihedral_angle_4_deg	16.934
r_dihedral_angle_3_deg	16.552
r_dihedral_angle_1_deg	7.464
r_scangle_it	2.129
r_angle_refined_deg	1.394
r_scbond_it	1.243
r_mcangle_it	1.162
r_angle_other_deg	0.886
r_mcbond_it	0.614
r_symmetry_vdw_other	0.262
r_symmetry_hbond_refined	0.248
r_nbd_refined	0.207
r_nbd_other	0.193
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.145
r_nbtor_other	0.087
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8333
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing