3DN9 | pdb_00003dn9

Carboxysome Subunit, CcmK1 C-terminal deletion mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BN4	PDB entry 3BN4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	1.6M ammonium sulfate, 0.1M MES, 10% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.204	α = 90.65
b = 49.194	β = 91.41
c = 49.211	γ = 91.43

Symmetry
Space Group	P 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	ADSC quantum Q315		2007-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0000000000	ALS	8.2.2

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	2.3	90	79.8	0.109	9.7	1.7		16303

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	2.3	2.38	42.8		0.433		1.3	866

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	PDB entry 3BN4	2.28	17.61	16255	816	77.41	0.224	0.222	0.22	0.274	0.27	RANDOM	34.204

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]
-0.02	-0.06		-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.517
r_dihedral_angle_4_deg	19.214
r_dihedral_angle_3_deg	16.427
r_dihedral_angle_1_deg	5.698
r_scangle_it	2.962
r_mcangle_it	2.839
r_scbond_it	2.03
r_mcbond_it	1.814
r_angle_refined_deg	1.093
r_angle_other_deg	0.846
r_mcbond_other	0.34
r_chiral_restr	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3966
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection