2OFM | pdb_00002ofm

1.11 A Crystal Structure of Apo Nitrophorin 4 From Rhodnius Prolixus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X80	PDB entry 1X80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	300	ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.47	α = 90
b = 42.816	β = 94.71
c = 52.72	γ = 90

Symmetry
Space Group	C 1 2 1

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		2005-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.11	17.4	93	0.06	0.06	25	2.8		63130			11.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.11		83		0.38	0.38	3.3	2.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	PDB entry 1X80	1.11	17.4	63130	56059	2984	96.76	0.14803	0.14621	0.16	0.18266	0.19	RANDOM	9.595

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]
0.17		-0.13	-0.21		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.234
r_dihedral_angle_3_deg	13.923
r_dihedral_angle_1_deg	7.824
r_dihedral_angle_4_deg	6.408
r_sphericity_free	4.774
r_scangle_it	2.971
r_sphericity_bonded	2.515
r_scbond_it	2.385
r_mcangle_it	1.86
r_angle_other_deg	1.749
r_angle_refined_deg	1.664
r_mcbond_it	1.468
r_rigid_bond_restr	1.154
r_mcbond_other	0.543
r_nbd_refined	0.486
r_xyhbond_nbd_other	0.427
r_xyhbond_nbd_refined	0.286
r_nbd_other	0.223
r_nbtor_refined	0.205
r_symmetry_vdw_other	0.205
r_symmetry_hbond_refined	0.188
r_symmetry_vdw_refined	0.183
r_chiral_restr	0.09
r_nbtor_other	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1909
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction