7MBL | pdb_00007mbl

Crystal structure of Equine Serum Albumin in complex with Cobalt (II)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	7.4	291	Protein: 1 uL of 34 mg/mL ESA dissolved in 10 mM Tris (pH 7.4) and 150 mM NaCl. Precipitant: 1 uL of 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M Tris pH 7.4. 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 3.3 uL of 50 mM cobalt (II) chloride dissolved in the reservoir solution were added directly to the 2 uL crystallization drop containing crystals to reach a final cobalt concentration of 31 mM and then incubated for a few hours before harvesting. Paratone was used as a cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.312	α = 90
b = 93.312	β = 90
c = 141.51	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 315r		2017-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97929	APS	19-BM

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	2.7	50	99.9	0.089	0.089	0.099	0.044	0.991	7.1	5		19239		-3	54.2

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	2.7	2.75	100		1.124	1.124	1.256	0.557	0.751	1.3	5.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5IIU	2.7	46.7	16913	928	92.88	0.2174	0.2133	0.22	0.2892	0.29	RANDOM	58.041

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]
-0.23	-0.11		-0.23		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.027
r_dihedral_angle_3_deg	17.26
r_dihedral_angle_4_deg	16.911
r_dihedral_angle_1_deg	5.947
r_angle_refined_deg	1.342
r_angle_other_deg	1.15
r_chiral_restr	0.058
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	4582
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data collection
MOLREP	phasing