4PWM | pdb_00004pwm

Crystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	436D	PDB ID 436D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	40 mM Na Cacodylate, 12 mM Spermine Tetrahydrochloride, 80 mM SrCl2, 10% MPD , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.25	α = 90
b = 41.34	β = 90
c = 66.41	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2013-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97920	APS	24-ID-C

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	1.95	26	97.5	0.045	16.26		5242	5113		3

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	1.95	2	99.5		0.62	2.8		385

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 ID 436D	1.95	25.89	4704	409	97.54	0.22492	0.22129	0.22	0.26721	0.27	RANDOM	45.709

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	8.229
r_long_range_B_other	8.218
r_scangle_other	7.305
r_scbond_it	5.348
r_scbond_other	5.346
r_angle_other_deg	3.717
r_angle_refined_deg	2.209
r_chiral_restr	0.164
r_gen_planes_refined	0.022
r_bond_refined_d	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	492
Solvent Atoms	12
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling