1SVD | pdb_00001svd

The structure of Halothiobacillus neapolitanus RuBisCo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RBL	pdb entry 1rbl

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	298	ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.68	53.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.066	α = 90
b = 157.066	β = 90
c = 107.609	γ = 90

Symmetry
Space Group	I 4 2 2

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 315	Double Crystal Si(111)	2003-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.1271	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	90		0.091	19.4	9.4	62138	62138

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	100		0.355	8.7	10.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MIR	THROUGHOUT	pdb entry 1rbl	1.8	87.71	58984	58984	3095	99.95	0.14608	0.14502	0.16	0.16574	0.18	RANDOM	11.186

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]
0.49			0.49		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.893
r_scangle_it	4.207
r_scbond_it	2.665
r_mcangle_it	1.759
r_angle_refined_deg	1.519
r_mcbond_it	0.945
r_angle_other_deg	0.91
r_symmetry_hbond_refined	0.307
r_symmetry_vdw_other	0.304
r_nbd_other	0.246
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.099
r_nbtor_other	0.085
r_gen_planes_other	0.022
r_bond_refined_d	0.015
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_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	4369
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing