2IJJ | pdb_00002ijj

Crystal structure analysis of ColE1 ROM mutant F14Y

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	273	Well solution: 22% MPD, 0.1 M sodium acetate pH 5.5, 0.1 M sodium chloride. Protein solution: protein 2.5 mg/ml, 0.01 M Tris pH 6.5, 0.05 M sodium chloride. Drops: equal volumes of well and protein solutions., VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.26	α = 90
b = 45.647	β = 90
c = 45.581	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	105	IMAGE PLATE	RIGAKU RAXIS IV	Blue Max-flux confocal	2005-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.89	20.01	98.6	0.047	16.3	4.94	17596	17351			28.4

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	1.89	1.96	93.1		0.293	3.8	4.69	1707

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	1ROP	1.9	20	16467	872	98.78	0.20625	0.20323	0.204	0.26257	0.2584	RANDOM	30.9

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]
-3.06			1.34		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.187
r_dihedral_angle_4_deg	21.463
r_dihedral_angle_3_deg	16.5
r_scangle_it	5.172
r_dihedral_angle_1_deg	5.145
r_scbond_it	3.371
r_mcangle_it	1.959
r_angle_refined_deg	1.643
r_mcbond_it	1.226
r_nbtor_refined	0.296
r_symmetry_hbond_refined	0.271
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.204
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.105
r_bond_refined_d	0.021
r_gen_planes_refined	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1369
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing