3KN8 | pdb_00003kn8

Crystal Structure of Haemophilus influenzae Y196A mutant Holo Ferric ion-Binding Protein A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D9V	PDB ENTRY 1D9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	28% PEG 550 MME, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.025	α = 90
b = 75.573	β = 90
c = 33.103	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	100	CCD	BRUKER SMART 6000		2002-07-06	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 Sym 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	62	92.32	0.049	9.94	3.05	21800	20126			20.802

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	2.03	92.32		0.2838	2.02

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 1D9V	1.89	62	20067	19046	1021	91.41	0.187	0.187	0.184	0.19	0.235	0.25	RANDOM	20.673

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]
-0.9			0.48		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.727
r_scangle_it	2.986
r_scbond_it	1.791
r_angle_refined_deg	1.155
r_mcangle_it	1.091
r_angle_other_deg	0.761
r_mcbond_it	0.594
r_symmetry_vdw_other	0.281
r_nbd_other	0.239
r_symmetry_vdw_refined	0.227
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.171
r_nbtor_other	0.084
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2273
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction