3BUJ | pdb_00003buj

Crystal Structure of CalO2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BVJ	Homology model derived from 2BVJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	MEPEG 5000, TMACl, Triethanolamine, pH 8.0, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.202	α = 90
b = 71.202	β = 90
c = 204.451	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9755	APS	21-ID-D

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	2.47	100	96.7	0.08	10.2	25.1		19109

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	2.47	2.56	77		0.475		12.4	1479

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	Homology model derived from 2BVJ	2.47	67.27	19078	976	96.89	0.201	0.198	0.1977	0.257	0.2542	RANDOM	32.593

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]
0.81			0.81		-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.684
r_dihedral_angle_3_deg	18.363
r_dihedral_angle_4_deg	18.295
r_dihedral_angle_1_deg	5.048
r_scangle_it	1.593
r_angle_refined_deg	1.175
r_scbond_it	1.01
r_mcangle_it	0.699
r_mcbond_it	0.399
r_symmetry_hbond_refined	0.382
r_nbtor_refined	0.303
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3096
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction