2VDI

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GK8	PDB ENTRY 1GK8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.09	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.831	α = 90
b = 178.206	β = 117.76
c = 122.917	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	CCD	MARRESEARCH		2002-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

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	2.65	20	88.7	0.12	10.4	12		118474

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	2.65	2.72	88.2		0.33	3.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GK8	2.65	20	112065	5907	88.7	0.206	0.205	0.234	RANDOM	15.24

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]
0.93		0.3	-0.03		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.243
r_dihedral_angle_4_deg	16.517
r_dihedral_angle_3_deg	15.645
r_dihedral_angle_1_deg	5.665
r_scangle_it	1.973
r_scbond_it	1.239
r_angle_refined_deg	1.114
r_mcangle_it	0.807
r_mcbond_it	0.493
r_symmetry_hbond_refined	0.417
r_symmetry_vdw_refined	0.314
r_nbtor_refined	0.305
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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_refined
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_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	38188
Nucleic Acid Atoms
Solvent Atoms	1538
Heterogen Atoms	348

Software

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