9ZMD | pdb_00009zmd

Equine Serum Albumin with Copper(II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MBL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	291.15	0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.4, 2.2 M ammonium sulfate, 5 mM copper(II) chloride mixed 1:1 with 36 mg/mL protein, 10 mM Tris-HCl, 150 mM sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.428	α = 90
b = 93.428	β = 90
c = 141.752	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	CCD	ADSC QUANTUM 210r		2015-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.28291	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.36	28	98.8	0.081	0.037	17.7	5.5		28717

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.4			0.48

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	2.65	26.985	20096	1013	98.529	0.194	0.1913	0.1939	0.2513	0.2528	35.847

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]
0.403	0.202		0.403		-1.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.296
r_dihedral_angle_6_deg	13.28
r_lrange_it	6.68
r_dihedral_angle_2_deg	6.457
r_lrange_other	6.4
r_dihedral_angle_1_deg	5.209
r_scangle_it	3.39
r_scangle_other	3.38
r_mcangle_it	2.788
r_mcangle_other	2.788
r_scbond_it	1.935
r_scbond_other	1.91
r_mcbond_it	1.608
r_mcbond_other	1.608
r_angle_refined_deg	1.067
r_angle_other_deg	0.416
r_nbd_other	0.333
r_symmetry_nbd_refined	0.283
r_nbd_refined	0.215
r_symmetry_nbd_other	0.196
r_metal_ion_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.156
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.06
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4603
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	43

Software

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