1NV9

HemK, apo structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NV8	PDB ENTRY 1NV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	292	PEG3000, Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.897	α = 90
b = 59.013	β = 90
c = 63.832	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	ADSC QUANTUM 4		2002-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97	SSRL	BL9-2

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	2.35	50	97.7	0.039	20		13364	13340

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)
	2.35	2.43	79.4		0.404	2.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	PDB ENTRY 1NV8	2.356	50	12707	12707	657	99.01	0.24166	0.24166	0.23869	0.30034	RANDOM	41.043

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]
			-3.61		3.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	22.235
r_dihedral_angle_1_deg	6.582
r_scangle_it	5.042
r_scbond_it	2.939
r_angle_refined_deg	2.611
r_mcangle_it	2.154
r_mcbond_it	1.175
r_angle_other_deg	1.088
r_symmetry_vdw_refined	0.408
r_symmetry_vdw_other	0.348
r_nbd_refined	0.297
r_symmetry_hbond_refined	0.282
r_nbd_other	0.255
r_xyhbond_nbd_refined	0.212
r_xyhbond_nbd_other	0.152
r_chiral_restr	0.151
r_nbtor_other	0.029
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2087
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing