4JB1 | pdb_00004jb1

Crystal structure of P. aeruginosa MurB in complex with NADP+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2MBR	PDB ENTRY 2MBR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	40 mM potassium phosphate, 20% v/v glycerol, 16% w/v PEG 8000 and 2 mM Tris-buffered NADP+ sodium salt, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.71	α = 90
b = 88.71	β = 90
c = 100.22	γ = 120

Symmetry
Space Group	P 61

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 210		2012-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

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	2.1	76.825	100	0.117	13.1	7.6	26203	26203	2.9	2.9

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	2.1	2.16	100		0.717	2.9	7.6	2179

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 2MBR	2.1	44.39	26176	26176	1325	99.99	0.1831	0.1831	0.1804	0.19	0.2363	0.23	RANDOM	41.8756

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]
1.29	1.29		1.29		-4.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.207
r_dihedral_angle_4_deg	18.079
r_dihedral_angle_3_deg	16.619
r_dihedral_angle_1_deg	7.393
r_mcangle_it	2.455
r_angle_refined_deg	2.125
r_mcbond_it	1.621
r_mcbond_other	1.621
r_angle_other_deg	0.9
r_chiral_restr	0.11
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2640
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	137

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
MOLREP	phasing