3ZXW | pdb_00003zxw

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		RUBISCO FROM TH.ELONGATUS WITHOUT LIGANDS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		80 MM HEPES, 20 MM MGCL2, 8% (W/V) PEG4000, 30% (V/V) GLYCEROL, PH=8

Crystal Properties
Matthews coefficient	Solvent content
2.4	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.5	α = 90
b = 111.5	β = 90
c = 397	γ = 90

Symmetry
Space Group	P 43 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	100	CCD	MARRESEARCH	MIRRORS	2009-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	2.1	20	98.7	0.11	14.9	7.7		144795		2

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	2.1	2.15	92		0.43	3.2	3.5

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	RUBISCO FROM TH.ELONGATUS WITHOUT LIGANDS	2.1	19.92	137341	7450	100	0.18276	0.18102	0.18	0.2135	0.21	RANDOM	35.997

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]
0.3			0.3		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.802
r_dihedral_angle_3_deg	13.182
r_dihedral_angle_4_deg	11.721
r_dihedral_angle_1_deg	5.339
r_scangle_it	2.867
r_scbond_it	1.762
r_mcangle_it	1.163
r_angle_refined_deg	1.013
r_mcbond_it	0.559
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17668
Nucleic Acid Atoms
Solvent Atoms	905
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing