2B3Y | pdb_00002b3y

Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.1	293	pH 8.1, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.91	α = 90
b = 215.47	β = 72
c = 64.01	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				2003-04-05	M	SINGLE WAVELENGTH
2	1	x-ray					2003-09-04	M	SINGLE WAVELENGTH
2,1	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4
2	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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
2,1	1.85	29.5	99	0.063	8.6	2		138110

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)
2,1	1.85	2	92.1		0.262	3	1.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2B3X	1.85	29.5	131161	6949	94	0.213	0.211	0.21	0.261	0.26	RANDOM	27.94

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]
-0.96		0.2	2.36		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.225
r_dihedral_angle_3_deg	16.068
r_dihedral_angle_4_deg	15.811
r_dihedral_angle_1_deg	5.89
r_scangle_it	4.108
r_scbond_it	3.168
r_mcangle_it	1.986
r_mcbond_it	1.485
r_angle_refined_deg	1.293
r_metal_ion_refined	0.337
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.225
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.198
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13856
Nucleic Acid Atoms
Solvent Atoms	970
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing