3Q23 | pdb_00003q23

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GMPCPP and Manganese: sustrate complex II

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	294	0.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25 % (DROP) 20% (RESERVOIR) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.834	α = 90
b = 111.861	β = 90
c = 276.093	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		2006-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

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	1.8	50	99	0.064	10.5	6	234419	234419	1	1

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)
	1.8	1.86	91.5		0.545		4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.8	50	234301	234301	11758	99	0.201	0.201	0.2	0.2	0.231	0.23	RANDOM	28

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]
0.99			-0.5		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.603
r_dihedral_angle_4_deg	16.038
r_dihedral_angle_3_deg	15.076
r_dihedral_angle_1_deg	4.8
r_scangle_it	1.843
r_scbond_it	1.163
r_angle_refined_deg	1.066
r_mcangle_it	0.819
r_mcbond_it	0.606
r_nbtor_refined	0.294
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.103
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.07
r_bond_refined_d	0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16897
Nucleic Acid Atoms	828
Solvent Atoms	2626
Heterogen Atoms	142

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing