Experiment: 3WQP

Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A12

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	293	Sodium Acetate 100mM (pH6.0), PEG 6000 5%(w/v), 2-methyl-1,4-pentanediol 10%(v/v), Calcium Chloride 120mM, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.566	α = 90
b = 246.238	β = 90
c = 144.628	γ = 90

Symmetry
Space Group	P 21 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	RAYONIX MX-225			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

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	2.25	50	99.9	0.09	13.1	7.4		287149

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	2.25	2.29	99.9		0.404	3.3

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	FOURIER SYNTHESIS	THROUGHOUT	3A12	2.25	50	286386	14396	99.61	0.222	0.2201	0.2152	0.2583	0.2501	RANDOM	51.496

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]
8.45			-4.19		-4.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.869
r_dihedral_angle_4_deg	17.78
r_dihedral_angle_3_deg	14.001
r_dihedral_angle_1_deg	5.108
r_angle_refined_deg	1.006
r_chiral_restr	0.069
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34306
Nucleic Acid Atoms
Solvent Atoms	2011
Heterogen Atoms	260

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing