2B3X | pdb_00002b3x

Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.352	α = 90
b = 103.307	β = 90
c = 225.957	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARRESEARCH		2004-02-26	M	MAD
2	1	100

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	1.741, 1.739, 1.283	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.54	113.23	94.6	0.079	0.079	11.1	3.5	28614	28614

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.54	113.23	27179	1435	96.88	0.183	0.18	0.18	0.225	0.23	RANDOM	32.466

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]
-0.36			-0.39		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.005
r_dihedral_angle_4_deg	18.255
r_dihedral_angle_3_deg	17.273
r_dihedral_angle_1_deg	5.822
r_scangle_it	2.079
r_scbond_it	1.414
r_mcangle_it	1.409
r_angle_refined_deg	1.23
r_mcbond_it	0.976
r_nbtor_refined	0.306
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.092
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6928
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	13

Software

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