3IB8 | pdb_00003ib8

Crystal structure of full length Rv0805 in complex with 5'-AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IB7	PDB ENTRY 3IB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Bis-Tris, amm. acetate, MPD, AMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.4	α = 90
b = 100.4	β = 90
c = 80.801	γ = 90

Symmetry
Space Group	P 41 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	MAR CCD 165 mm	mirrors	2006-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9864	EMBL/DESY, HAMBURG	BW7A

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	99.9	0.067	9.7	8		38865	3	3	29.1

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	1.8	1.84	100		0.619	3.8	7.7	2546

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 3IB7	1.8	31.75	45158	38804	3868	99.93	0.217	0.152	0.15	0.1498	0.168	0.1693	RANDOM	27.65

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]
-0.84			-0.84		1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.908
r_dihedral_angle_4_deg	11.802
r_dihedral_angle_3_deg	11.205
r_dihedral_angle_1_deg	5.491
r_scangle_it	2.078
r_scbond_it	1.279
r_angle_refined_deg	1.237
r_mcangle_it	0.64
r_mcbond_it	0.401
r_nbtor_refined	0.297
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.106
r_chiral_restr	0.078
r_symmetry_hbond_refined	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2229
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	67

Software

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